Protein Domain Annotations of the SARS-CoV-2 Proteomics as a Blue-Print for Mapping the Features for Drug and Vaccine Designs

2020 ◽  
Vol 25 (2) ◽  
pp. 26-32
Author(s):  
Arli Parikesit ◽  
Keyword(s):  
Drug Design ◽  
Vaccine Design ◽  
Causal Agent ◽  
Protein Domain ◽  
Potential Drug ◽  
Potential Target ◽  
Conserved Domain ◽  
Drug Lead ◽  
Blue Print ◽  
Domain Database

SARS-CoV-2 virus, as the causal agent for the COVID-19 pandemic, remains an enigma in the bioinformatics sense. Current efforts in drug and vaccine design in primarily targeting general devised protein domain while overlooking the specific features in the proteomics repertoire. However, the NCBI Conserved Domain Database (CDD) could annotate the specific features that are indispensable for a more advanced drug and vaccine design. In this regard, the annotation efforts were initiated with CDD database, and visualized with the 3D Protein Visualizer of Cn3D. The exsistence of the ATP and ADP binding protein with respected domains were found to be a very potential target for drug design. It is recommended that nucleoside inhibitor that could mimick the ATP molecule could serve as a potential drug lead agains SARS-CoV-2.

scholarly journals NCBI's Conserved Domain Database and Tools for Protein Domain Analysis

2019 ◽  
Vol 69 (1) ◽  
Author(s):  
Mingzhang Yang ◽  
Myra K. Derbyshire ◽  
Roxanne A. Yamashita ◽  
Aron Marchler‐Bauer
Keyword(s):  
Domain Analysis ◽  
Protein Domain ◽  
Conserved Domain ◽  
Domain Database

Protein domain hierarchy Gibbs sampling strategies

2014 ◽  
Vol 13 (4) ◽  
Author(s):  
Andrew F. Neuwald
Keyword(s):  
Gibbs Sampling ◽  
Sequence Alignment ◽  
Gibbs Sampler ◽  
Multiple Sequence Alignment ◽  
Protein Domain ◽  
Sampling Strategies ◽  
Multiple Sequence ◽  
Manual Curation ◽  
Conserved Domain ◽  
Domain Database

AbstractHierarchically-arranged multiple sequence alignment profiles are useful for modeling protein domains that have functionally diverged into evolutionarily-related subgroups. Currently such alignment hierarchies are largely constructed through manual curation, as for the NCBI Conserved Domain Database (CDD). Recently, however, I developed a Gibbs sampler that uses an approach termed

scholarly journals CDD/SPARCLE: the conserved domain database in 2020

2019 ◽  
Vol 48 (D1) ◽  
pp. D265-D268 ◽  
Author(s):  
Shennan Lu ◽  
Jiyao Wang ◽  
Farideh Chitsaz ◽  
Myra K Derbyshire ◽  
Renata C Geer ◽  
...  
Keyword(s):  
Protein Domain ◽  
Molecular Function ◽  
Protein Families ◽  
Bacterial Proteins ◽  
Protein Architecture ◽  
Conserved Domain ◽  
Single Protein ◽  
Domain Database ◽  
User Queries

Abstract As NLM’s Conserved Domain Database (CDD) enters its 20th year of operations as a publicly available resource, CDD curation staff continues to develop hierarchical classifications of widely distributed protein domain families, and to record conserved sites associated with molecular function, so that they can be mapped onto user queries in support of hypothesis-driven biomolecular research. CDD offers both an archive of pre-computed domain annotations as well as live search services for both single protein or nucleotide queries and larger sets of protein query sequences. CDD staff has continued to characterize protein families via conserved domain architectures and has built up a significant corpus of curated domain architectures in support of naming bacterial proteins in RefSeq. These architecture definitions are available via SPARCLE, the Subfamily Protein Architecture Labeling Engine. CDD can be accessed at https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml.

Pradimicin-S is a Highly Soluble Non-peptidic Small-size Carbohydrate-binding Antibiotic that may Qualify as a Potential Drug Lead for HIV Treatment

2009 ◽  
Vol 82 (2) ◽  
pp. A44
Author(s):  
J. Balzarini ◽  
K. François ◽  
K. Van Laethem ◽  
B. Hoorelbeke ◽  
J. Auwerx ◽  
...  
Keyword(s):  
Hiv Treatment ◽  
Carbohydrate Binding ◽  
Potential Drug ◽  
Drug Lead

An in silico study: Novel targets for potential drug and vaccine design against drug resistant H. pylori

2018 ◽  
Vol 122 ◽  
pp. 156-161 ◽  
Author(s):  
Chiranjeevi Pasala ◽  
Chandra Sekhar Reddy Chilamakuri ◽  
Sudheer Kumar Katari ◽  
Ravina Madhulitha Nalamolu ◽  
Aparna R. Bitla ◽  
...  
Keyword(s):  
In Silico ◽  
Vaccine Design ◽  
Drug Resistant ◽  
Potential Drug ◽  
In Silico Study ◽  
Novel Targets ◽  
H Pylori

scholarly journals Crystal Structure of African Swine Fever Virus dUTPase Reveals a Potential Drug Target

mBio ◽  
2019 ◽  
Vol 10 (5) ◽  
Author(s):  
Changyao Li ◽  
Yan Chai ◽  
Hao Song ◽  
Changjiang Weng ◽  
Jianxun Qi ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Mycobacterium Tuberculosis ◽  
High Resolution ◽  
Drug Design ◽  
Active Site ◽  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Fever Virus ◽  
Potential Drug ◽  
Content Type

ABSTRACT E165R, a highly specific dUTP nucleotidohydrolase (dUTPase) encoded by the African swine fever virus (ASFV) genome, is required for productive replication of ASFV in swine macrophages. Here, we solved the high-resolution crystal structures of E165R in its apo state and in complex with its product dUMP. Structural analysis explicitly defined the architecture of the active site of the enzyme as well as the interaction between the active site and the dUMP ligand. By comparing the ASFV E165R structure with dUTPase structures from other species, we found that the active site of E165R is highly similar to those of dUTPases from Mycobacterium tuberculosis and Plasmodium falciparum, against which small-molecule chemicals have been developed, which could be the potential drug or lead compound candidates for ASFV. Our results provide important basis for anti-ASFV drug design by targeting E165R. IMPORTANCE African swine fever virus (ASFV), an Asfivirus affecting pigs and wild boars with up to 100% case fatality rate, is currently rampaging throughout China and some other countries in Asia. There is an urgent need to develop therapeutic and preventive reagents against the virus. Our crystallographic and biochemical studies reveal that ASFV E165R is a member of trimeric dUTP nucleotidohydrolase (dUTPase) family that catalyzes the hydrolysis of dUTP into dUMP. Our apo-E165R and E165R-dUMP structures reveal the constitutive residues and the configuration of the active center of this enzyme in rich detail and give evidence that the active center of E165R is very similar to that of dUTPases from Plasmodium falciparum and Mycobacterium tuberculosis, which have already been used as targets for designing drugs. Therefore, our high-resolution structures of E165R provide useful structural information for chemotherapeutic drug design.

scholarly journals Frontispiece: A Short‐Lived but Highly Cytotoxic Vanadium(V) Complex as a Potential Drug Lead for Brain Cancer Treatment by Intratumoral Injections

2020 ◽  
Vol 59 (37) ◽  
Author(s):  
Aviva Levina ◽  
Adriana Pires Vieira ◽  
Asanka Wijetunga ◽  
Ravinder Kaur ◽  
Jordan T. Koehn ◽  
...  
Keyword(s):  
Cancer Treatment ◽  
Brain Cancer ◽  
Potential Drug ◽  
Drug Lead ◽  
Intratumoral Injections

Surface proteins, potential drug target for antiviral therapy against Nipah virus and in silico drug design

2011 ◽  
Vol 44 (13) ◽  
pp. S34 ◽  
Author(s):  
Rafiqur Rahman ◽  
S.M. Mahbubbur Rashid ◽  
Manzur Sayeem ◽  
Istiaq Sharif ◽  
Kawsar Sharif
Keyword(s):  
Drug Design ◽  
Antiviral Therapy ◽  
In Silico ◽  
Drug Target ◽  
Nipah Virus ◽  
Surface Proteins ◽  
Potential Drug Target ◽  
Potential Drug ◽  
In Silico Drug Design

scholarly journals CDD: specific functional annotation with the Conserved Domain Database

2009 ◽  
Vol 37 (Database) ◽  
pp. D205-D210 ◽  
Author(s):  
A. Marchler-Bauer ◽  
J. B. Anderson ◽  
F. Chitsaz ◽  
M. K. Derbyshire ◽  
C. DeWeese-Scott ◽  
...  
Keyword(s):  
Functional Annotation ◽  
Conserved Domain ◽  
Domain Database
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