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Journal ArticleDOI: 10.1080/07391102.2020.1734485

Anti-dengue infectivity evaluation of bioflavonoid from Azadirachta indica by dengue virus serine protease inhibition.

04 Mar 2021-Journal of Biomolecular Structure & Dynamics (Taylor & Francis)-Vol. 39, Iss: 4, pp 1417-1430
Abstract: Dengue virus (DENV) serine protease enzyme, i.e. NS2B-NS3pro (non-structural protein 2B-non-structural protein 3) has been approved as prime drug target for the drug discovery against dengue infect...

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Topics: Dengue virus (67%), Dengue fever (55%), Infectivity (50%) ... show more

20 results found

Open accessJournal ArticleDOI: 10.1080/07391102.2020.1842807
Abstract: Recent outbreak of COVID-19 pandemic caused by severe acute respiratory syndrome-Coronavirus-2 (SARS-CoV-2) has raised serious global concern for public health. The viral main 3-chymotrypsin-like c...

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27 Citations

Journal ArticleDOI: 10.1080/07391102.2020.1747545
Abstract: Recent Zika virus (ZIKV) outbreak and association with human diseases such as neurological disorders have raised global health concerns. However, in the absence of an approved anti-ZIKV drug has ge...

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Topics: Zika virus (56%)

13 Citations

Journal ArticleDOI: 10.1016/J.MOLLIQ.2020.113322
Shiv Bharadwaj1, Kyung Eun Lee1, Vivek Dhar Dwivedi, Umesh Yadava2  +2 moreInstitutions (3)
Abstract: Matrix metalloproteinases (MMPs) actively caused enzymatic proteolysis of extracellular matrix (ECM) and cell surface proteins, suggested as critical for connective tissue that results in progressive aging and other diseases. Numerous efforts have been conducted to design the broadrange of synthetic inhibitors for MMPs, but none of them have successfully passed the clinical trials. Recently, Ganoderma lucidum triterpenoids were reported with significant medicinal beneficial effects, including free radical-scavengers and anti-cancer activity. However, their concealed property as an antagonist of MMPs is not yet explored. Hence, this study attempts to elucidate the Ganoderma lucidum triterpenoids potential as broad range of MMPs inhibitor using computational chemistry approaches. Herein, 100 Ganoderma lucidum triterpenoids were virtually screened against the model MMPs, i.e. gelatinase (MMP2), stromelysin (MMP3), collagenase (MMP8), and metalloelastase (MMP12) followed by ADME profiling, and results into the prediction of 14 bioactive triterpenoids as broad-spectrum MMPs inhibitors. Furthermore, stringent extra precision molecular docking by Glide protocol revealed Ganoderiol D and Ganodermanotriol as potential antagonists of model MMPs. These triterpenoids were further studied by density functional methods and in docked complexes of MMPs using molecular dynamics simulation, predicted the non-reactivity of triterpenoids, and established the MMPs-triterpenoids complex stability by strong intermolecular interactions (hydrogen bonds, hydrophobic and polar interactions), respectively. Furthermore, binding free energy calculations deduced the significant involvement of coulomb and van der Waals forces in the respective MMP-triterpenoid complexes stability, supported the Ganoderiol D and Ganodermanotriol as broad range antagonist of MMPs.

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Topics: Ganoderiol (52%)

10 Citations

Open accessJournal ArticleDOI: 10.1080/07391102.2020.1834457
Abstract: A novel coronavirus (SARS-CoV2) has caused a major outbreak in humans around the globe, and it became a severe threat to human healthcare than all other infectious diseases. Researchers were urged to discover and test various approaches to control and prevent such a deadly disease. Considering the emergency and necessity, we screened reported antiviral compounds present in the traditional Indian medicinal plants for the inhibition of SARS-CoV2 main protease. In this study, we used molecular docking to screen 41 reported antiviral compounds that exist in Indian medicinal plants and shown amentoflavone from the plant Torreyanucifera with a higher docking score. Furthermore, we performed a 40 ns atomic molecular dynamics simulation and free binding energy calculations to explore the stability of the top five protein-ligand complexes. Through the article, we insist that the amentoflavone, hypericin and Torvoside H from the traditional Indian medicinal plants may be used as a potential inhibitor of SARS-CoV2 main protease and further biochemical experiments could shed light on understanding the mechanism of inhibition by these plant-derived antiviral compounds. Communicated by Ramaswamy H. Sarma.

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8 Citations


58 results found

Open accessJournal ArticleDOI: 10.1139/P80-159
Abstract: We assess various approximate forms for the correlation energy per particle of the spin-polarized homogeneous electron gas that have frequently been used in applications of the local spin density a...

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Topics: Electron liquid (56%), Spin-½ (55%), Orbital-free density functional theory (53%) ... show more

16,835 Citations

Journal ArticleDOI: 10.1021/JA00214A001
Abstract: A complete set of intermolecular potential functions has been developed for use in computer simulations of proteins in their native environment. Parameters are reported for 25 peptide residues as well as the common neutral and charged terminal groups. The potential functions have the simple Coulomb plus Lennard-Jones form and are compatible with the widely used models for water, TIP4P, TIP3P, and SPC. The parameters were obtained and tested primarily in conjunction with Monte Carlo statistical mechanics simulations of 36 pure organic liquids and numerous aqueous solutions of organic ions representative of subunits in the side chains and backbones of proteins. Bond stretch, angle bend, and torsional terms have been adopted from the AMBER united-atom force field. As reported here, further testing has involved studies of conformational energy surfaces and optimizations of the crystal structures for four cyclic hexapeptides and a cyclic pentapeptide. The average root-mean-square deviation from the X-ray structures of the crystals is only 0.17 A for the atomic positions and 3% for the unit cell volumes. A more critical test was then provided by performing energy minimizations for the complete crystal of the protein crambin, including 182 water molecules that were initially placed via a Monte Carlo simulation. The resultant root-mean-square deviation for the non-hydrogen atoms is still ca. 0.2 A and the variation in the errors for charged, polar, and nonpolar residues is small. Improvement is apparent over the AMBER united-atom force field which has previously been demonstrated to be superior to many alternatives. Computer simulations are undoubtedly destined to became an increasingly important means for investigating the structures and dynamics of biomolecular systems.' At the heart of such theoretical calculations are the force fields that describe the interatomic interactions and the mechanics of deformations of the molecules.* There is also little doubt that there will be a continual evolution in force fields with added complexity and improved performance paralleling the availability of computer resources. Our own efforts in this area over the last few years have resulted in the OPLS potential functions for proteins whose development and performance are summarized here. These potential functions have a simple form and they have been parametrized directly to reproduce experimental thermodynamic and structural data on fluids. Consequently, they are computationally efficient and their description of proteins in solution or crystalline environments should be superior to many alterantives that have been developed with limited condensed-phase data. The latter point is pursued here primarily through calculations on the crystal structures for four cyclic hexapeptides, a cyclic pentapeptide, and the protein crambin. Improvements are apparent in comparison to the AMBER united-atom force field3 which has previously been shown to be superior to many alternative^.^ (1) Beveridge, D. L., Jorgensen, W. L., Eds. Ann. N.Y. Acad. Sci. 1986, 482. ( 2 ) For reviews, see: (a) Levitt, M. Annu. Reu. Biophys. Eioeng. 1982, 11, 251. (b) McCammon, J. A. Rep. Prog. Phys. 1984, 47, 1. (3) Weiner, S. J.; Kollman, P. A.; Case, D. A,; Singh, U. C.; Ghio, C.; Alagona, G.; Profeta, S.; Weiner, P. J. Am. Chem. SOC. 1984, 106, 765. Parametrization The peptide residues of proteins contain readily identifiable organic subunits such as amides, hydrocarbons, alcohols, thioethers, etc. In view of this and since data are available on the corresponding pure organic liquids, our approach to developing a force field for proteins was to build it up from parameters demonstrated to yield good descriptions of organic liquids. U1timately, the force field would need to treat both intramolecular terms for bond stretches, angle bends, and torsions, as well as the intermolecular and intramolecular nonbonded interactions. The latter are generally accepted to be the most difficult part of the problem and have been our focus.3 A simple, computationally efficient form was chosen to represent the nonbonded interactions through Coulomb and Lennard-Jones terms interacting between sites centered on nuclei (eq 1). Thus, the intermolecular inter-

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Topics: Crambin (62%)

3,960 Citations

Open accessJournal ArticleDOI: 10.1128/CMR.11.3.480
Duane J. Gubler1Institutions (1)
Abstract: Dengue fever, a very old disease, has reemerged in the past 20 years with an expanded geographic distribution of both the viruses and the mosquito vectors, increased epidemic activity, the development of hyperendemicity (the cocirculation of multiple serotypes), and the emergence of dengue hemorrhagic fever in new geographic regions. In 1998 this mosquito-borne disease is the most important tropical infectious disease after malaria, with an estimated 100 million cases of dengue fever, 500,000 cases of dengue hemorrhagic fever, and 25,000 deaths annually. The reasons for this resurgence and emergence of dengue hemorrhagic fever in the waning years of the 20th century are complex and not fully understood, but demographic, societal, and public health infrastructure changes in the past 30 years have contributed greatly. This paper reviews the changing epidemiology of dengue and dengue hemorrhagic fever by geographic region, the natural history and transmission cycles, clinical diagnosis of both dengue fever and dengue hemorrhagic fever, serologic and virologic laboratory diagnoses, pathogenesis, surveillance, prevention, and control. A major challenge for public health officials in all tropical areas of the world is to devleop and implement sustainable prevention and control programs that will reverse the trend of emergent dengue hemorrhagic fever.

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Topics: 2009 Bolivian dengue fever epidemic (75%), Dengue vaccine (71%), Dengue fever (71%) ... show more

3,706 Citations

Open access
01 Jan 2014-
Topics: Dengue fever (67%)

2,588 Citations

Proceedings ArticleDOI: 10.1145/1188455.1188544
Kevin J. Bowers1, Edmond Chow1, Huafeng Xu1, Ron O. Dror1  +9 moreInstitutions (1)
11 Nov 2006-
Abstract: Although molecular dynamics (MD) simulations of biomolecular systems often run for days to months, many events of great scientific interest and pharmaceutical relevance occur on long time scales that remain beyond reach. We present several new algorithms and implementation techniques that significantly accelerate parallel MD simulations compared with current stateof- the-art codes. These include a novel parallel decomposition method and message-passing techniques that reduce communication requirements, as well as novel communication primitives that further reduce communication time. We have also developed numerical techniques that maintain high accuracy while using single precision computation in order to exploit processor-level vector instructions. These methods are embodied in a newly developed MD code called Desmond that achieves unprecedented simulation throughput and parallel scalability on commodity clusters. Our results suggest that Desmond?s parallel performance substantially surpasses that of any previously described code. For example, on a standard benchmark, Desmond?s performance on a conventional Opteron cluster with 2K processors slightly exceeded the reported performance of IBM?s Blue Gene/L machine with 32K processors running its Blue Matter MD code.

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1,472 Citations