SciDBMaker: new software for computer-aided design of specialized biological databases

DCTPep, the data of cancer therapy peptides

With the discovery of the therapeutic activity of peptides, they have emerged as a promising class of anti-cancer agents due to their specific targeting, low toxicity, and potential for high selectivity. In particular, as peptide-drug conjugates enter clinical, the coupling of targeted peptides with traditional chemotherapy drugs or cytotoxic agents will become a new direction in cancer treatment. To facilitate the drug development of cancer therapy peptides, we have constructed DCTPep, a novel, open, and comprehensive database for cancer therapy peptides. In addition to traditional anticancer peptides (ACPs), the peptide library also includes peptides related to cancer therapy. These data were collected manually from published research articles, patents, and other protein or peptide databases. Data on drug library include clinically investigated and/or approved peptide drugs related to cancer therapy, which mainly come from the portal websites of drug regulatory authorities and organisations in different countries and regions. DCTPep has a total of 6214 entries, we believe that DCTPep will contribute to the design and screening of future cancer therapy peptides.

DRAVP: A Comprehensive Database of Antiviral Peptides and Proteins

Viruses with rapid replication and easy mutation can become resistant to antiviral drug treatment. With novel viral infections emerging, such as the recent COVID-19 pandemic, novel antiviral therapies are urgently needed. Antiviral proteins, such as interferon, have been used for treating chronic hepatitis C infections for decades. Natural-origin antimicrobial peptides, such as defensins, have also been identified as possessing antiviral activities, including direct antiviral effects and the ability to induce indirect immune responses to viruses. To promote the development of antiviral drugs, we constructed a data repository of antiviral peptides and proteins (DRAVP). The database provides general information, antiviral activity, structure information, physicochemical information, and literature information for peptides and proteins. Because most of the proteins and peptides lack experimentally determined structures, AlphaFold was used to predict each antiviral peptide's structure. A free website for users (http://dravp.cpu-bioinfor.org/, accessed on 30 August 2022) was constructed to facilitate data retrieval and sequence analysis. Additionally, all the data can be accessed from the web interface. The DRAVP database aims to be a useful resource for developing antiviral drugs.

HORDB a comprehensive database of peptide hormones

Peptide hormones (also known as hormone peptides and polypeptide hormones) are hormones composed of peptides and are signal transduction molecules produced by a class of multicellular organisms. It plays an important role in the physiological and behavioral regulation of animals and humans as well as in the growth of plants. In order to promote the research on peptide hormones, we constructed HORDB database. The database currently has a total of 6024 entries, including 5729 peptide hormones, 40 peptide drugs and 255 marketed pharmaceutical preparations information. Each entry provided comprehensive information related to the peptide, including general information, sequence, activity, structure, physical information and literature information. We also added information on IC50, EC50, ED50, target, and whether or not the blood-brain barrier was crossed to the activity information note. In addition, HORDB integrates search and sequence analysis to facilitate user browsing and data analysis. We believe that the peptide hormones information collected by HORDB will promote the design and discovery of peptide hormones, All data are hosted and available in figshare https://doi.org/10.6084/m9.figshare.c.5522241 .

Antimicrobial Potential of the Genera Geobacillus and Parageobacillus, as Well as Endolysins Biosynthesized by Their Bacteriophages

In the recent decades, antibiotic resistance has emerged and spread rapidly among clinically relevant pathogens. The natural ability of bacteria to transmit resistance determinants through horizontal gene transfer poses constant challenges to drug development. Natural molecules produced by soil microorganisms continue to be a key source of new antimicrobial agents. In this context, bacteria from the Geobacillus and Parageobacillus genera deserve special attention. Although there is commercial and industrial interest in these microorganisms, the full range of antibacterial compounds biosynthesized by the Geobacillus and Parageobacillus species remains largely unexplored. The aim of this review is to present the strong antimicrobial potential of these bacteria and endolysins produced by their bacteriophages.

Inhibition of methicillin-resistant Staphylococcus aureus (MRSA) by antimicrobial peptides (AMPs) and plant essential oils

CONTEXT

Drug-resistant bacterial infections cause considerable patient mortality and morbidity. The annual frequency of deaths from methicillin-resistant Staphylococcus aureus (MRSA) has surpassed those caused by human immunodeficiency virus/acquired immune deficiency syndrome. The antimicrobial peptides (AMPs), plant essential oils (EOs) and their combinations have proven to be quite effective in killing a wide selection of bacterial pathogens including MRSA.

OBJECTIVES

This review summarizes the studies in the use of AMPs, plant EOs and their combinations for coping with MRSA bacteria, and to formulate new prospects for future studies on this topic.

METHODS

The sources of scientific literature such as PubMed, library search, Google Scholar, Science Direct and electronic databases such as 'The Antimicrobial Peptide Database', 'Collection of Anti-Microbial Peptides' and 'YADAMP'. Physicochemical data of anti-MRSA peptides were determined by Scientific DataBase Maker software.

RESULTS

Of the 118 peptides, 88 exhibited an activity against MRSA with the highest activity of minimum inhibitory concentration values. Various plant EOs have been effective against MRSA. Remarkably, lemongrass EOs completely inhibited all MRSA growth on the plate. Lemon myrtle, Mountain savory, Cinnamon bark and Melissa EOs showed a significant inhibition.

CONCLUSION

Several of these AMPs, EOs and their combinations were effective against MRSA. Their activities have implications for the development of new drugs for medical use.

Strand-biased gene distribution, purine assymetry and environmental factors influence protein evolution in Bacillus

A strong purine asymmetry, along with strand-biased gene distribution and the presence of PolC, prevails in Bacillus and some other members of Firmicutes, Fusobacteria and Tenericutes. The analysis of protein features in 21 Bacillus species of diverse metabolic, virulence and ecological traits revealed that purine asymmetry in conjunction with lineage/niche specific constraints significantly influences protein evolution in Bacillus. All Bacillus species, except for Se-respiring Bacillus selenitireducens, display distinct strand-specific biases in amino acid usage, which may affect the isoelectric point or surface charge distribution of proteins with prevalence of acidic and basic residues in the leading and lagging strand proteins, respectively.

Use of SciDBMaker as Tool for the Design of Specialized Biological Databases

The exponential growth of molecular biology research in recent decades has brought concomitant growth in the number and size of genomic and proteomic databases used to interpret experimental findings. Particularly, growth of protein sequence records created the need for smaller and manually annotated databases. Since scientists are continually developing new specific databases to enhance their understanding of biological processes, the authors created SciDBMaker to provide a tool for easy building of new specialized protein knowledge bases. This chapter also suggests best practices for specialized biological databases design, and provides examples for the implementation of these practices.

Aptamer Base: a collaborative knowledge base to describe aptamers and SELEX experiments

Over the past several decades, rapid developments in both molecular and information technology have collectively increased our ability to understand molecular recognition. One emerging area of interest in molecular recognition research includes the isolation of aptamers. Aptamers are single-stranded nucleic acid or amino acid polymers that recognize and bind to targets with high affinity and selectivity. While research has focused on collecting aptamers and their interactions, most of the information regarding experimental methods remains in the unstructured and textual format of peer reviewed publications. To address this, we present the Aptamer Base, a database that provides detailed, structured information about the experimental conditions under which aptamers were selected and their binding affinity quantified. The open collaborative nature of the Aptamer Base provides the community with a unique resource that can be updated and curated in a decentralized manner, thereby accommodating the ever evolving field of aptamer research.

Database URL:http://aptamer.freebase.com

Current trends in antimicrobial agent research: chemo- and bioinformatics approaches

Databases and chemo- and bioinformatics tools that contain genomic, proteomic and functional information have become indispensable for antimicrobial drug research. The combination of chemoinformatics tools, bioinformatics tools and relational databases provides means of analyzing, linking and comparing online search results. The development of computational tools feeds on a diversity of disciplines, including mathematics, statistics, computer science, information technology and molecular biology. The computational approach to antimicrobial agent discovery and design encompasses genomics, molecular simulation and dynamics, molecular docking, structural and/or functional class prediction, and quantitative structure-activity relationships. This article reviews progress in the development of computational methods, tools and databases used for organizing and extracting biological meaning from antimicrobial research.

BACTIBASE second release: a database and tool platform for bacteriocin characterization

BACKGROUND

BACTIBASE is an integrated open-access database designed for the characterization of bacterial antimicrobial peptides, commonly known as bacteriocins.

DESCRIPTION

For its second release, BACTIBASE has been expanded and equipped with additional functions aimed at both casual and power users. The number of entries has been increased by 44% and includes data collected from published literature as well as high-throughput datasets. The database provides a manually curated annotation of bacteriocin sequences. Improvements brought to BACTIBASE include incorporation of various tools for bacteriocin analysis, such as homology search, multiple sequence alignments, Hidden Markov Models, molecular modelling and retrieval through our taxonomy Browser.

CONCLUSION

The provided features should make BACTIBASE a useful tool in food preservation or food safety applications and could have implications for the development of new drugs for medical use. BACTIBASE is available at http://bactibase.pfba-lab-tun.org.

PhytAMP: a database dedicated to antimicrobial plant peptides

Plants produce small cysteine-rich antimicrobial peptides as an innate defense against pathogens. Based on amino acid sequence homology, these peptides were classified mostly as α-defensins, thionins, lipid transfer proteins, cyclotides, snakins and hevein-like. Although many antimicrobial plant peptides are now well characterized, much information is still missing or is unavailable to potential users. The compilation of such information in one centralized resource, such as a database would therefore facilitate the study of the potential these peptide structures represent, for example, as alternatives in response to increasing antibiotic resistance or for increasing plant resistance to pathogens by genetic engineering. To achieve this goal, we developed a new database, PhytAMP, which contains valuable information on antimicrobial plant peptides, including taxonomic, microbiological and physicochemical data. Information is very easy to extract from this database and allows rapid prediction of structure/function relationships and target organisms and hence better exploitation of plant peptide biological activities in both the pharmaceutical and agricultural sectors. PhytAMP may be accessed free of charge at http://phytamp.pfba-lab.org.