Abstract:
:3CL proteases (3CLpro) are only found in RNA viruses and have a central role in polyprotein processing during replication. Therefore, 3CLpro has emerged as promising drug target for therapeutic treatment of infections caused by Coronaviruses. In the light of the recent major outbreak of the SARS-CoV-2 virus and the continuously rising numbers of infections and casualties, there is an urgent need for quickly available drugs or vaccines to stop the current COVID-19 pandemic. Repurposing of approved drugs as 3CLpro inhibitors could dramatically shorten the period up to approval as therapeutic against SARS-CoV-2, since pharmacokinetics and toxicity is already known. Several known drugs, e.g. oxytetracycline, doxorubicin, kanamycin, cefpiramide, teniposide, proanthocyanidin and salvianolic acid B, but also not-approved active compounds from the ZINC15 library were identified as new potential inhibitors of 3CLpro by using different complementary virtual screening and docking approaches. These compounds have the potential to be further optimized using structure based drug design as demonstrated for oxytetracycline.
journal_name
Comput Biol Chemjournal_title
Computational biology and chemistryauthors
Meyer-Almes FJdoi
10.1016/j.compbiolchem.2020.107351subject
Has Abstractpub_date
2020-10-01 00:00:00pages
107351eissn
1476-9271issn
1476-928Xpii
S1476-9271(20)30704-0journal_volume
88pub_type
杂志文章abstract::With the development of cancer research, various gene expression datasets containing cancer information show an explosive growth trend. In addition, due to the continuous maturity of single-cell RNA sequencing (scRNA-seq) technology, the protein information and pedigree information of a single cell are also continuous...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2020.107368
更新日期:2020-12-01 00:00:00
abstract::A computational inestigation on the difference in colors of two plants 'Peony' and 'Morning glory' by the same pigment 'Peonidin' has been performed by means of absorption characteristics. Peonidin imparts purple color to the flowers in Peony and blue to that in Morning glory. TDDFT tool in Gaussian 09 software packag...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2018.07.015
更新日期:2018-10-01 00:00:00
abstract::Adenosine deaminase (ADA) is an enzyme involved in purine metabolism. ADA converts adenosine to inosine and liberates ammonia. Because of their critical role in the differentiation and maturation of cells, the regulation of ADA activity is considered as a potential therapeutic approach to prevent malignant and inflamm...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2016.08.005
更新日期:2016-10-01 00:00:00
abstract::Monoamine oxidase (MAO) enzymes are one of the most promising targets for the treatment of neurological disorders. A series of phenylisoxazole carbohydrazides was designed, synthesized and screened for both MAO-A and MAO-B inhibition using Amplex Red assays. None of the compounds inhibited the MAO-A activity while mos...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2019.01.012
更新日期:2019-04-01 00:00:00
abstract::The occurrence of similar structural repeats in a protein structure has evolved through gene duplication. These repeats act as a structural building block and form more than one compact structural and functional unit called a repeat domain. The protein families comprising similar structural repeats are mainly involved...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2010.03.006
更新日期:2010-04-01 00:00:00
abstract::Epigallocatechin gallate, a flavonoid from Camellia sinensis possess various pharmacological activities such as anticancer, antimicrobial and antioxidant etc. Adenosine deaminase, (ADA), is a key enzyme involved in the purine metabolism, the inhibitors of which is being considered as highly promising candidate for the...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2019.107111
更新日期:2019-12-01 00:00:00
abstract::Reptin functions in a wide range of biological processes including chromatin remodelling, nucleolar organization and transcriptional regulation of WNT signalling. As β-catenin dependent transcriptional repression and activation events involve binding of Reptin and histone deacetylase 1 to APPL endocytic proteins, this...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2013.05.005
更新日期:2013-12-01 00:00:00
abstract::Zinc fingers are small protein domains in which zinc plays a structural role, contributing to the stability of the zinc-peptide complex. Zinc fingers are structurally diverse and are present in proteins that perform a broad range of functions in various cellular processes, such as replication and repair, transcription...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2018.03.005
更新日期:2018-06-01 00:00:00
abstract::MicroRNAs are important negative regulators of gene expression in higher eukaryotes. The miRNA repertoire of the closest human animal relative, the chimpanzee (Pan troglodytes), is largely unknown. In this study, we focused on computational search of novel miRNA homologs in chimpanzee. We have searched and analyzed th...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2008.07.024
更新日期:2009-02-01 00:00:00
abstract::Beta-secretase is a potential target for inhibitory drugs against Alzheimer's disease as it cleaves amyloid precursor protein (APP) to form insoluble amyloid plaques and vascular deposits in the brain. Beta-secretase is matured from its precursor protein, called beta-secretase zymogen, which, different from most of ot...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2007.03.007
更新日期:2007-06-01 00:00:00
abstract::Functional classification of genes represents one of the most basic problems in genome analysis and annotation. Our analysis of some of the popular methods for functional classification of genes shows that these methods are not always consistent with each other and may not be specific enough for high-resolution gene f...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2008.02.007
更新日期:2008-06-01 00:00:00
abstract::Caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the COVID-19 pandemic is ongoing, with no proven safe and effective vaccine to date. Further, effective therapeutic agents for COVID-19 are limited, and as a result, the identification of potential small molecule antiviral drugs is of particul...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2020.107408
更新日期:2020-12-01 00:00:00
abstract::With advances in genomics, transcriptomics, metabolomics and proteomics, and more expansive electronic clinical record monitoring, as well as advances in computation, we have entered the Big Data era in biomedical research. Data gathering is growing rapidly while only a small fraction of this data is converted to usef...
journal_title:Computational biology and chemistry
pub_type: 杂志文章,评审
doi:10.1016/j.compbiolchem.2015.08.005
更新日期:2015-12-01 00:00:00
abstract::The concept of chaos being radically different from statistical randomness is introduced into chemometrics research. The chaotic system that is deterministic with underlying patterns and inherent ability in searching the space of interest has been employed to improve the performance of chemometric algorithms. In this ...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/s1476-9271(02)00083-x
更新日期:2003-07-01 00:00:00
abstract::In this study, the structural and antioxidant behavior of the three lichen-derived natural compounds such as atranorin (AT), evernic acid (EV) and diffractaic acid (DF) has been investigated in the gas and water phase using both B3LYP and M06-2X functional level of density functional theory (DFT) with two different ba...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2019.03.009
更新日期:2019-06-01 00:00:00
abstract::The NS2B-NS3 protease is essential for the replication process of Dengue Virus, which make it an attractive target for anti-virus drugs. Since a considerable number of NS2B-NS3 protease inhibitors have been reported so far, it is significant for the discovery of more effective antivirus compounds with the essential st...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2018.09.010
更新日期:2018-12-01 00:00:00
abstract::Alzheimer's disease (AD) is a progressive neurodegenerative disease of central nervous system among elderly people. Human acetylcholinesterase (hAChE), an important enzyme in neuronal signaling, is responsible for the degradation of acetylcholine which in turn prevents the post synaptic signal transmissions. hAChE has...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2017.04.002
更新日期:2017-06-01 00:00:00
abstract::Detection of protein complexes is very important to understand the principles of cellular organization and function. Recently, large protein-protein interactions (PPIs) networks have become available using high-throughput experimental techniques. These networks make it possible to develop computational methods for pro...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2015.07.012
更新日期:2015-10-01 00:00:00
abstract::Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disorder, and its pathogenesis in males and in cases without accompanying lupus nephritis (LN-) is not fully understood. In this study, we identified 90 (82 up- and 8 downregulated) differentially expressed genes (DEGs) common to female LN-, female LN+ a...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2019.107135
更新日期:2019-12-01 00:00:00
abstract::The induced pluripotent cells (iPSCs) are derived from somatic cells by reprogramming their genetic profiles. Such a process requires coordinated dynamic expression of hundreds of genes and proteins. As both deterministic and stochastic elements control the reprogramming process, it is not easy to have a way to reflec...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2011.05.002
更新日期:2011-08-10 00:00:00
abstract::A computational study of the interaction of cardiac troponin I (cTnI) with its specific antibody and of that antibody with skeletal troponin I (sTnI), the principal interferon of cTnI, is carried out. Computational and simulation tools such as FTSite, FTMap, FTDock and pyDock are used to determine the binding sites of...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2019.04.002
更新日期:2019-06-01 00:00:00
abstract::Pseudomonas aeruginosa is an opportunistic gram-negative bacterium that has the capability to acquire resistance under hostile conditions and become a threat worldwide. It is involved in nosocomial infections. In the current study, potential novel drug targets against P. aeruginosa have been identified using core prot...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2018.02.017
更新日期:2018-06-01 00:00:00
abstract::The potential of using sole respirometric CO2 labeling measurement for 13C metabolic flux analysis was investigated by metabolic simulations. For this purpose a model was created, considering all CO2 forming and consuming reactions in the central catabolic and anabolic pathways. To facilitate the interpretation of the...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2005.02.005
更新日期:2005-04-01 00:00:00
abstract::Tamoxifen is a prodrug and cytochrome P450 2C9 (CYP2C9) has a significant role in the formation of a therapeutically more potent metabolite (4-hydroxytamoxifen) than tamoxifen. Since CYP2C9 exhibits genetic polymorphism, it may contribute to different phenotypic drug response. Moreover, it may be misleading if the pos...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2019.107166
更新日期:2020-02-01 00:00:00
abstract::Development in two-dimensional (2D) drug-delivery materials have quickly translated into biological and pharmacological fields. In this present work, pristine graphene (PG) and hexagonal boron nitride (h-BN) sheets are explored as a drug carrier for cytarabine (CYT) and clofarabine (CLF) anti-cancer drugs using densit...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2020.107334
更新日期:2020-10-01 00:00:00
abstract::G protein-coupled receptors (GPCRs), a large eukaryotic protein family, have proved difficult to comprehensively detect and functionally identify by homology searches and domain detection, because they are highly divergent and their sequences share strikingly little similarity. Transmembrane (TM) topology pattern anal...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2003.11.003
更新日期:2004-02-01 00:00:00
abstract::Protein structure prediction is considered as one of the most challenging and computationally intractable combinatorial problem. Thus, the efficient modeling of convoluted search space, the clever use of energy functions, and more importantly, the use of effective sampling algorithms become crucial to address this pro...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2016.01.008
更新日期:2016-04-01 00:00:00
abstract::Cytosine methylation is one of the most important RNA epigenetic modifications. With the development of experimental technology, scientists attach more importance to RNA cytosine methylation and find bisulfite sequencing is an effective experimental method for RNA cytosine methylation study. However, there are only a ...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2016.09.003
更新日期:2016-12-01 00:00:00
abstract::Real-time RT-PCR has been frequently used in quantitative research in molecular biology and bioinformatics. It provides remarkably useful technology to assess expression of genes. Although mathematical models for gene amplification process have been studied, statistical models and methods for data analysis in real-tim...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2005.10.005
更新日期:2006-02-01 00:00:00
abstract::Programmed cell death or apoptosis plays a vital physiological role in the development and homeostasis. Any discrepancy in apoptosis may trigger testicular and neurodegenerative diseases, ischemic damage, autoimmune disorders and many types of cancer. Tcte3 (T-complex testis expressed 3) is an accessory component of a...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2014.10.005
更新日期:2014-12-01 00:00:00