Abstract:
:SARS-CoV-2 cause fatal infection in 213 countries accounting for the death of millions of people globally. In the present study, phytochemicals from spices were assessed for their ability to interact with SARS-CoV-2 MPro. Structure based virtual screening was performed with 146 phytochemicals from spices using Autodock Vina. Phytochemicals with binding energy ≥ -8.0 kcal/mol were selected to understand their interaction with MPro. Virtual screening was further validated by performing molecular docking to generate favorable docked poses and the participation of important amino acid residues. Molecular dynamics simulation for the docked poses was performed to study thermodynamic properties of the protein, ligand and protein-ligand complexes. The finding shows that cinnamtannin B2 and cyanin showed favorable binding affinity values with SARS-CoV-2 MPro. The results are comparable in terms of docked poses, important amino acid participation and thermodynamic properties with the standard control drugs remdesivir, benazepril and hydroxychloroquine diphosphate. Prime MM-GBSA was employed for end-point binding energy calculation. Binding to domain I and II of MPro were mediated through the OH, SH, NH2 and non-polar side chain of amino acids. Cinnamtannin B2 and cyanin binds to MPro with many sub sites within the active site with RMSD and RMSF within 4 Å. The results computed using Prime MM-GBSA show that cinnamtannin B2 (-68.54940214 kcal/mol) and cyanin (-62.1902835 kcal/mol) have better binding affinity in comparison to hydroxychloroquine diphosphate (-54.00912412 kcal/mol) and benazepril (-53.70242369 kcal/mol). The results provide a basis for exploiting cinnamtannin B2 and cyanin as a starting point potential candidate for the development of drug against SARS-CoV-2. Communicated by Ramaswamy H. Sarma.
journal_name
J Biomol Struct Dynjournal_title
Journal of biomolecular structure & dynamicsauthors
Rajendran M,Roy S,Ravichandran K,Mishra B,Gupta DK,Nagarajan S,Arul Selvaraj RC,Provaznik Idoi
10.1080/07391102.2020.1845980subject
Has Abstractpub_date
2020-11-17 00:00:00pages
1-15eissn
0739-1102issn
1538-0254pub_type
杂志文章abstract::The assembly and maturation of viruses with icosahedral capsids must be coordinated with icosahedral symmetry. The icosahedral symmetry imposes also the restrictions on the cooperative specific interactions between genomic RNA/DNA and coat proteins that should be reflected in quasi-regular segmentation of viral genomi...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2018.1479660
更新日期:2019-06-01 00:00:00
abstract::Geometry optimizations and energy calculations have been carried out via molecular orbital methods at the density functional B3LYP/LANL2DZ level on the molecules PO3-, OPO3(3-), HOPO3(2-), CH3OPO3(2-), H(CH3OPO3)-, O(PO3)2(4-), HO(PO3)2(3-), CH2(PO3)2(4-), (CH3OPO2)O(PO3)3-, O(PO3)3(5-), HO(PO3)3(4-), (PO3)3(3-), (CH3...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2000.10506655
更新日期:2000-08-01 00:00:00
abstract::Nuclear quadrupole relaxation is a sensitive measure of electrolyte environments. We used the relaxation of 23Na to probe mobile ion-matrix interactions and the electrostatic structure of the polyelectrolyte extracellular matrix of cartilage. Specifically, we measured spin-lattice and spin-spin relaxation times of 23N...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1996.10508898
更新日期:1996-04-01 00:00:00
abstract::The recent COVID-19 pandemic caused by SARS-CoV-2 has recorded a high number of infected people across the globe. The virulent nature of the virus makes it necessary for us to identify promising therapeutic agents in a time-sensitive manner. The current study utilises an in silico based drug repurposing approach to id...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1814870
更新日期:2020-09-04 00:00:00
abstract::Mycobacterium tuberculosis (Mtb), the pathogen of tuberculosis (TB), is one of the most infectious bacteria in the world. The traditional strategy to combat TB involves targeting the pathogen directly; however, the rapid evolution of drug resistance lessens the efficiency of this anti-TB method. Therefore, in recent y...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2016.1157037
更新日期:2017-02-01 00:00:00
abstract::Communicated by Ramaswamy H. Sarma. ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 信件
doi:10.1080/07391102.2020.1733090
更新日期:2020-03-03 00:00:00
abstract::A simplified multidimensional search was applied to determine the structure of deoxyhexamer CGCGCG in the crystal form belonging to the space group C222(1) (a = 45.6 A, b = 37.3 A, c = 70.3 A). This crystal form contains two Z-DNA duplexes per asymmetric unit in a similar orientation. The search consists of several ma...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1994.10508052
更新日期:1994-04-01 00:00:00
abstract::Sickle cell disease is caused by the amino acid substitution of glutamic acid to valine, which leads to the polymerization of deoxygenated sickle hemoglobin (HbS) into long strands. These strands are responsible for the sickling of red blood cells (RBCs), making blood hyper-coagulable leading to an increased chance of...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2018.1456362
更新日期:2019-03-01 00:00:00
abstract::Cold shock proteins (CSPs) are ancient nucleic acid-binding proteins and well conserved from bacteria to animals as well as plants. In prokaryotes, CSPs possess a single cold shock domain (CSD) while animal CSPs, flanked by N- and C-terminal domains, are commonly named Y-box proteins. Interestingly, the plants CSPs co...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2014.907747
更新日期:2015-01-01 00:00:00
abstract::Inhibition of heat shock protein 90 (Hsp90) is known to be a significantly effective strategy in cancer therapy. Here, pyrazolopyranopyrimidine derivatives were characterized as new Hsp90 inhibitors. The molecules' key structure (ZINC02819805) was determined by utilizing a pharmacophore model virtual screening workflo...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2019.1660216
更新日期:2020-08-01 00:00:00
abstract::Proton ENDOR has been observed from frozen solutions (ca. 38K degrees) of copper meso-(4-N-tetra-methylpyridyl)porphyrin (CuTMpyP(4)) complexed with Salmon sperm DNA in water and D2O. Lines from exchangeable protons of the DNA bases have been observed in these ENDOR spectra. Analyses of these ENDOR data show that the ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1992.10507962
更新日期:1992-04-01 00:00:00
abstract::The mechanism by which peptides bind to micelles is believed to be a two-phase process, involving (i). initial electrostatic interactions between the peptide and micelle surface, followed by (ii). hydrophobic interactions between peptide side chains and the micelle core. To better characterize the electrostatic portio...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2004.10506949
更新日期:2004-02-01 00:00:00
abstract::In the course of studies related to new molecules with intercalative properties, we have been led to design and synthesize a bithiazole derivative, namely the 2-phenyl-6-[2'-(4'-(ethoxy-carbonyl)thiazolyl)]thiazolo[3,2- b][1,2,4]triazole (PETT). Its interaction with calf thymus DNA was studied using thermal denaturati...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1986.10506341
更新日期:1986-10-01 00:00:00
abstract::Many bacterial genomes have been sequenced and stored in public databases now, of which Reference Sequence (RefSeq) is the most widely used one. However, the annotation in RefSeq is still unsatisfactory. The present analysis is focused on the re-annotation of an important plant pathogen genome Xanthomonas oryzae pv. o...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2012.698218
更新日期:2013-03-01 00:00:00
abstract::Alkylamine-substituted naphthalene imides and diimides bind DNA by intercalation and have applications as anticancer agents. The unique structures of these imides in which two adjacent carbonyl groups lie coplanar to an extended aromatic ring system allow the possibility of sequence-selective interactions between the ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1996.10508128
更新日期:1996-12-01 00:00:00
abstract::Molecular mechanics and molecular dynamics studies are performed to investigate the conformational preference of cell surface higher gangliosides (GT1A and GT1B) and their interaction with Cholera Toxin. The water mediated hydrogen bonding network exists between sugar residues in gangliosides. An integrated molecular ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2006.10507089
更新日期:2006-06-01 00:00:00
abstract::It is well known that the biological activity of gallated proanthocyanidins (PAs) is highly structure-dependent. Polymerization degree (DP) and linkage types affect their biological activity greatly. Positions and orientations of gallated PAs in lipid bilayer reveal their structure-function activity at the molecular l...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2017.1369163
更新日期:2018-08-01 00:00:00
abstract::Partial proteolysis of the lambda cI repressor has been carried out systematically with trypsin, chymotrypsin, elastase, endoproteinase Glu-C, kallikrein, and thrombin. The cleavage sites have been determined by (i) comparison of fragments produced and observed in SDS-polyacrylamide gel with known fragments and plots ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2008.10507249
更新日期:2008-12-01 00:00:00
abstract::Understanding, at the molecular level, the effect of AMPs on biological membranes is of crucial importance given the increasing number of multidrug-resistant bacteria. Being part of an ancient type of innate immunity system, AMPs have emerged as a potential solution for which bacteria have not developed resistance. Tr...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1867640
更新日期:2021-01-05 00:00:00
abstract::Cytochrome bcc complex is important for ATP synthesis and cellular activity, as a crucial step in the terminal reduction of oxygen in aerobic electron transport chains. The b subunit of cytochrome bcc complex (QcrB) has been reported as a promising anti-tuberculosis target, with many novel anti-tuberculosis scaffolds ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2019.1688196
更新日期:2020-10-01 00:00:00
abstract::Silk materials are receiving significant attention as base materials for various functional nanomaterials and nanodevices, due to its exceptionally high mechanical properties, biocompatibility, and degradable characteristics. Although crystalline silk regions are composed of various repetitive motifs with differing am...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2017.1323015
更新日期:2018-04-01 00:00:00
abstract::Human major histocompatibility complex class I (MHC I) - or human leukocyte antigen (HLA) - proteins present intracellularly processed peptides to cytotoxic T lymphocytes in the adaptive immune response to pathogens. A high level of polymorphism in human MHC I proteins defines the peptide-binding specificity of thousa...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2017.1295884
更新日期:2018-02-01 00:00:00
abstract::Donepezil is an acetylcholinesterase inhibitor (AChEI) in use to treat symptomatic patients of mild to moderate Alzheimer's disease (AD). Ferritin is an iron protein associated with storage and sequestration of excess ferrous iron in a way maintaining proper function of cellular processes and plays a key role in AD si...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1851302
更新日期:2020-11-23 00:00:00
abstract::The operator-binding domain of the lambda-repressor contains five alpha-helices and an extended N-terminal arm in the crystal structure determined by Pabo and Lewis reported in Nature 298, 443, 1982 (1). The four helices form a "box" enclosing a hydrophobic core with the fifth helix interacting with the equivalent hel...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1984.10507515
更新日期:1984-03-01 00:00:00
abstract::In search of suitable therapy for the management of Alzheimer's disease, this study was designed to evaluate metal complexes against its biochemical targets. Zinc metal carboxylates (AAZ1-AAZ6) were evaluated against acetylcholinesterase (AChE) and butyrylcholinesterase (BChE). The antioxidant in combination with anti...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1724569
更新日期:2020-02-13 00:00:00
abstract::The so-called CCAAT box is believed to be a major promoter element of higher eukaryotes though it is ill-defined being deduced from very limited sequence data. The comprehensive computer analysis of an unbiased set of 168 promoters presented here removes several of the persisting uncertainties. In particular, it delin...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1988.10506466
更新日期:1988-06-01 00:00:00
abstract::Abstract Aromatic stacking of nucleic acid bases is one of the key players in determining the structure and dynamics of nucleic acids. The arrangement of nucleic acid bases with extensive overlap of their aromatic rings gave rise to numerous often contradictory suggestions about the physical origins of stacking and ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章,评审
doi:10.1080/07391102.2000.10506597
更新日期:2000-01-01 00:00:00
abstract::The results of 1-nanosecond molecular dynamics simulations of the enzyme ribonuclease T1 and its 2'GMP complex in water are presented. A classification of the angular reorientations of the backbone amide groups is achieved via a transformation of NH-vector trajectories into several coordinate frames, thus unravelling ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1994.10508074
更新日期:1994-06-01 00:00:00
abstract::The hexachlorocyclotriphosphaze compound (N3P3Cl6, HCCP) was reacted with excess (E)-(1-(4'-oxyphenyl)-3-(substituted-phenyl)prop-2-en-1-ones (2-11) to produce hexakis[(1-(4-oxyphenyl)-3-(substituted-phenyl)prop-2-en-1-one)]cyclotriphosphazenes (CP 2-11). The structures of products (CP 2-11) were confirmed using eleme...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1846621
更新日期:2020-11-19 00:00:00
abstract::The aim of this study was to attempt to determine the extent to which the chemical shifts of the nonexchangeable base protons of a DNA helix depend upon the base sequence. We measured the proton NMR spectra of twelve decadeoxynucleotides in order to carry out a "statistical" treatment. In the helices, the chemical shi...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1988.10506434
更新日期:1988-02-01 00:00:00