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. 2020 Jun 25;15(6):e0235193. doi: 10.1371/journal.pone.0235193

ACD: Antimicrobial chemotherapeutics database

Mohd W Azam 1, Amit Kumar 1, Asad U Khan 1,*
Editor: Timir Tripathi2
PMCID: PMC7316249  PMID: 32584882

Abstract

Antimicrobial resistance is becoming a growing health problem, which has become a challenge for the physicians to control infection and also an economic burden on the healthcare. This increase in resistance to the present antimicrobial agents led the researchers to find some alternative and more efficient drugs which can fight with the resistant microorganisms more effectively. Hence, in silico approach is used to design some novel drugs against various targets of microorganisms. For effective virtual screening of the drugs, there is a need to know about the chemical structure and properties of the antimicrobial agents. Therefore, we have prepared a comprehensive database as a platform for the researcher to search for possible lead molecules. Antimicrobial chemotherapeutics database (ACD) is comprised of ~4100 synthetic antimicrobial compounds as well as ~1030 active antimicrobial peptides. The Antimicrobial peptides are mainly from biological sources but some of them are synthetic in nature. Only those compounds, which are found to be active against either bacteria (both Gram-positive and negative) or fungus, are selected for this database.The ACD database is freely available at URL: http://amdr.amu.ac.in/acd, and it is compatible with desktops, smartphones, and tablets.

Introduction

The ineffectiveness of antimicrobial agents, i.e. antimicrobial resistance (AMR), has become a global public health threat. A large number of bacterial species have been reported to have resistant markers against different antibiotics. Klebsiella pneumoniae, E. coli, Staphlylococcus aureus, Mycobacterium, Streptococcus pneumoniae, etc., are some of the common species involved in infections [1–3]. It is a great menace to the patients having organ transplantation, major surgeries like hip transplant, breast biopsy, caesarean sections and cancer chemotherapies where the risk of spreading infection is high. Besides this, antimicrobial resistance (AMR) causes prolonged treatment of the disease and an enhanced cost of treatment [4]. As per WHO MDR-TB factsheet 2018 report about 558,000 new cases of multi-drug resistance tuberculosis (MDR-TB) have been estimated in 2017 and 161,000 cases of MDR or RR-TB have been detected and reported in 2017 [5]. The MRSA (Methicillin-resistant Staphylococcus aureus) infected people are 64% more likely to die than the people infected with non-resistant strains as per the WHO report [4].

CDC report of 2019 on antibiotic-resistance threats in the United States, showed that 2.8 million antibiotic-resistant infections reported every year, due to which is resulted in 35,000 deaths per year and a huge economic loss to the country [6]. European Centre For Disease Prevention and Control (ECDC) report on the bacterial challenge: "time to react", estimated about 25,000 people who have died due to antibiotic resistance problem in Europe, Iceland, and Norway, during 2007. Moreover, infection due to the antibiotic-resistant bacteria was responsible for staying patients in the hospital, extra 2.5 million days in Europe, Iceland and Norway, and these extra days may cost more than EUR 900 million [7].

There is a need to search novel effective lead molecules for future drug candidates against the antimicrobial-resistant microorganisms. In view of the above-described situation, we have developed a manually curated database of antimicrobial molecules (ACD), comprises of both synthetic chemical compounds and the antimicrobial peptides. These peptides were isolated mainly from biological sources along with some synthetic peptides. There are many databases available for antimicrobial peptides like CAMP (http://www.camp.bicnirrh.res.in/) [8], APD3 (http://aps.unmc.edu/AP/main.php) [9], PhytAMP (http://phytamp.pfba-lab-tun.org/main.php) [10] and similarly, a large number of databases are available for chemical compounds like PubChem (https://pubchem.ncbi.nlm.nih.gov/) [11], DrugBank (https://www.drugbank.ca/) [12], ZINC (http://zinc.docking.org/) [13], ChemDB (http://www.chemdb.com/) [14], etc., but none of the above databases provided a single platform where a user can get access to both synthetic chemical molecules and antimicrobial peptides. The purpose of this database was to provide a single user-friendly platform where a user can get information on both the synthetic compounds as well as the antimicrobial peptides. In ACD database, only the effective antimicrobial (compounds and peptides) agents were selected for the database. It makes easier to select the putative drug candidate. Further, this database is comprehensive in nature and provides multiple ways to find out the molecule of interest. In spite of this, the user can get good information about the properties of the molecule. The contemporary databases of ACD are generally based on data, which is very vast and nonspecific in nature, which may lead to time consuming and reduced work efficiency. The synthetic compound and antimicrobial peptide on a single platform will help researchers to go for virtual screening to identify effective lead molecules in minimum time.

Materials and methods

Data collection

The data collection of chemical compounds was made from the available databases ZINC [13], DrugBank [12], ChemDB [14], PubChem [11], PubChem Bioassays [15], and literature search. The antimicrobial peptides were collected from various sources like extensive literature searches from PubMed and some from Uniprot (Fig 1). The whole data of both synthetic compounds and antimicrobial compounds are collected based on their antibacterial and antifungal activity. Of the total data collected, about 2900 antibacterial, 1200 synthetic antifungal compounds, and about 1030 active antimicrobial peptides were selected (Fig 2).

Fig 1. Antimicrobial chemotherapeutics database architecture.

Fig 1

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Fig 2. Schematic representation of total compounds and peptides available in ACD.

Fig 2

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The data of each synthetic compound is arranged into two categories: the first category gives information about the name and identifier of the compound (compound name, target, CBD ID, Zinc ID, PubChem ID, Canonical SMILES, IUPAC Name, ISO Smiles and Bioassay) and the second category provides information about chemical and physical properties of the compound (Molecular weight, Molecular Formula, XLogP, hydrogen bond acceptor, hydrogen bond donor and Rotatable bond).

The peptide data is categorized based on antibacterial and antifungal activity. Further, the antibacterial peptides are divided into Gram-positive and Gram-negative. The user can also get information about the peptide length, charge, target, peptide sequence, the source of the peptide, i.e. the organism from which the peptide was collected, and also a brief description of the peptide with ACD ID.

Database framework and user interface

ACD was built on Apache Tomcat Server 7.0.76 (http://tomcat.apache.org/) over MVC Architecture with Java1.7 web technologies servlets and JSP (https://java.com/). The database tables are stored in MySQL Server 5.0 relational database. MySQL technology was preferred as they are open-source software and a platform-independent, web application developed by Java can be configured with many application servers, such as Apache Tomcat, WebLogic, JBoss, and WebSphere. Tomcat, a platform for web applications with tools for configuration and management, is freely available. Interfaces in the ACD database are designed in a user-friendly manner using the Bootstrap 3.0 UI Framework that allows for easy navigation over almost all kind of devices.

A brief user interface is given below:

Home

In this section, the various features of the ACD database are displayed through which the user can enter into its desirable section.

Compounds

This section deals with the synthetic antimicrobial molecules, which are categorized into antibacterial and antifungal agents. The user can search both antibacterial and antifungal compounds by their names, properties (viz. molecular weight, rotatable bond, H-acceptor, H-donor, and X LogP values) or by a desirable percentage of structural similarity.

Peptide

This database deals with the antimicrobial peptides, which can be searched by their antibacterial activity (Gram-positive or Gram-negative), antifungal activity, peptide name or by properties of a peptide, e.g. peptide sequence, peptide length, net charge, etc. Reference and a brief description of each peptide were also provided.

Assistance

In this section, a user can get instructions and guide to using the various features, included in the database.

Team

Information is given regarding the team members involved in the database construction.

Contact us

Contact details of the authors are given in this section. The user can contact the authors for any query regarding the database and also can give their valuable suggestions.

Results

Data access

The data access in the ACD database is easy to handle. The synthetic antimicrobial compounds can be searched through antibacterial, antifungal activities, as well as by drawing structure using JSME editor and can also compress the results by specifying the percent structural similarity threshold. Each search of the synthetic compound provides information about the compound, e.g. target organisms name with its particular target if available, PubChem ID link, as well as PubChem bioassay link, are also provided so that user can visit directly to the respective databases. The user can also download the 2D SDF or 3D SDF files of the desired compound. The image of each compound was also provided.

The antimicrobial peptides were given in a separate peptide section. To make easy access to desirable peptide, we have provided several property searches, like target activity, i.e. Gram-positive, Gram-negative, antifungal, peptide length, the net charge of the peptide. The peptide sequences, a brief description of the peptide with reported MIC (mg/ml) values of most of the peptides and the references, were also given.

Tools

JSME

With the help of JavaScript Molecular Editor (JSME), one can also draw the molecular structure of the compound to search the structural similarity [16].

JSmol

3D molecular structures of the chemical compounds can be viewed through JSmol.

Conclusion

To get-rid-of global threat of antimicrobial resistance, a need of an hour is to translate the drug research into effective medicine. High throughput screening and validation of antimicrobial agents are required to combat this global problem. Therefore, the ACD database was designed to provide a user-friendly and convenient resource for the researcher to identify novel antimicrobial agents. The ACD database provides a single platform of both antimicrobial chemical compounds and peptides. It provides several user-friendly search tools and methods, which makes the finding of the specific drug candidate much easier than other databases. A wide range of properties and structure similarity search of synthetic compounds were given so that the user can find its desirable compounds quite easily. Similarly, the effective antimicrobial peptides were selected for this database with their several properties as described earlier. The database will save time and effort of students and researchers to search for potential antimicrobial agents as future drug candidates.

Update

The database will be updated regularly with new information and data entries from time to time. The authors and developers of this database will appreciate any comments, valuable suggestions, and queries from the users of this database.

Acknowledgments

We would like to thank Dr. Peter Ertl for providing us Java Script Molecular Editor (JSME) [16] for our Database.

Data Availability

All relevant data are within the paper.

Funding Statement

The author(s) received no specific funding for this work.

References

Decision Letter 0

Timir Tripathi

19 May 2020

PONE-D-20-12977

ACD: Antimicrobial chemotherapeutics database

PLOS ONE

Dear Dr. Khan,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

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We look forward to receiving your revised manuscript.

Kind regards,

Timir Tripathi, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments:

The database is important and the work is good but the manuscript is too short. Both reviewer feel that the manuscript may be expanded for the benefit of readers.

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

**********

2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: N/A

Reviewer #2: Yes

**********

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #2: Yes

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5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: Manuscript Title: ACD: Antimicrobial chemotherapeutics database

Manuscript Number: PONE-D-20-12977

The ACD database is required as it clubs the properties of many important and significant databases from the prospect of antibacterial resistance.

The manuscript may be accepted with minor changes.

1.Slight syntax errors like ….”time to react ”…. there should be no space after react.; second line of second paragraph, font is different (antibiotic resistance); full form of ECDC should be given;

2. …..and very few are synthetic….This line in the abstract may be rewritten with better sentence format.

3.There should be the same format for heading. Most of them are in Capital sentences while a few are in Capital Word like Data Collection. There should be a uniformity in the entire manuscript.

4.As per 2014 WHO report…….updated data of MDR-TB should be provided. Data of 2014 is quite old for a database.

5.Tha abstract may be re-written as it is showing high similarity with the author's web page (amdr.amu.ac.in).

6.Introduction may be elaborated with more emphasis on the need of this database.

7.Comparison of available databases may be discussed in more detail. Further, compare this database with other available databases. Although the ACD database provides more information than current databases, a detail is required on the syntax of the database. Tools used to create ACD may be discussed with other databases and compare the limits and advantages of this database with other similar databases.

8.Its an excellent database so its appication and competativeness of the server should also be highlighted.

Reviewer #2: In the present database, "ACD: Antimicrobial chemotherapeutics database" author have collected huge informatios about antimicrobial compounds, and compiled it in this database. I my view it will be very useful for researcher working in the field of antimicrobial drug resistance. I have tried this database with two compounds and found positive results. I recommend this dataset for publication in PLOS ONE after two minor suggestions (If possible)

1.Add an option of search compound based on .SDF file of compound (if possible)

2.Add an option to search based on the peptide sequence (if possible)

**********

6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: Yes: Dr. Asimul Islam

Reviewer #2: No

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PLoS One. 2020 Jun 25;15(6):e0235193. doi: 10.1371/journal.pone.0235193.r002

Author response to Decision Letter 0

22 May 2020

Justification of reviewers’ comments

Note: all changes are yellow highlighted

Reviewr 1: The ACD database is required as it clubs the properties of many important and significant databases from the prospect of antibacterial resistance.

The manuscript may be accepted with minor changes.

1. Slight syntax errors like ….”time to react ”…. there should be no space after react.; second line of second paragraph, font is different (antibiotic resistance); full form of ECDC should be given;

Compliance: Remove space after react

"antibiotic resistance" is written in another format instead Times New Roman

ECDC: European Centre For Disease Prevention and Control

2. …..and very few are synthetic….This line in the abstract may be rewritten with better sentence format.

Compliance: ….. as per suggestion modified “Antimicrobial chemotherapeutics database (ACD) is comprised of ~4100 synthetic antimicrobial compounds as well as ~1030 active antimicrobial peptides. The Antimicrobial peptides are mainly from biological sources and some of them are synthetic in nature.”

3. There should be the same format for heading. Most of them are in Capital sentences while a few are in Capital Word like Data

Collection. There should be a uniformity in the entire manuscript.

Compliance:: modified as suggested by reviewr.

4. As per 2014 WHO report…….updated data of MDR-TB should be provided. Data of 2014 is quite old for a database.

Compliance: recent data of WHO was updated and an additional reference was also included in the text as below.

“treatment [4]. As per WHO MDR-TB factsheet 2018 report about 558,000 new cases of multi-drug resistance tuberculosis (MDR-TB) have been estimated in 2017 and 161,000 cases of MDR or RR TB detected and reported in 2017 [5]. The MRSA (Methicillin-resistant Staphylococcus aureus) infected people are 64% more likely to die than the people infected with non-resistant strains as per the WHO report [4].”

5. Tha abstract may be re-written as it is showing high similarity with the author's web page (amdr.amu.ac.in).

Compliance: abstract is modified as suggested by the reviewer

6. Introduction may be elaborated with more emphasis on the need of this database.

Compliance: Introduction is modified as suggested by the reviewer

7. Comparison of available databases may be discussed in more detail. Further, compare this database with other available databases. Although the ACD database provides more information than current databases, a detail is required on the syntax of the database. Tools used to create ACD may be discussed with other databases and compare the limits and advantages of this database with other similar databases.

Compliance: some additional advantages of the ACD database were didcussed along with tools used to attain the objectives.

8. Its an excellent database so its appication and competativeness of the server should also be highlighted.

Compliance: Introduction and conclusion section is modified accordingly.

Reviewer #2: In the present database, "ACD: Antimicrobial chemotherapeutics database" author have collected huge informatios about antimicrobial compounds, and compiled it in this database. I my view it will be very useful for researcher working in the field of antimicrobial drug resistance. I have tried this database with two compounds and found positive results. I recommend this dataset for publication in PLOS ONE after two minor suggestions (If possible)

1.Add an option of search compound based on .SDF file of compound (if possible)

2.Add an option to search based on the peptide sequence (if possible)

Compliance: I agree with the wornderful suggestion of reviewer but due to lock down no lab is allowed to open, students are not allowed to visit labs. It may take some time to add these featrures. But that may be added even after the study publishd. any way we keep updateing the daatbase. I assure reviewer that these features will be added later. Any way data base will remain active and functional to suffise the need of resaerchers.

Attachment

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Decision Letter 1

Timir Tripathi

11 Jun 2020

ACD: Antimicrobial chemotherapeutics database

PONE-D-20-12977R1

Dear Dr. Khan,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org.

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Kind regards,

Timir Tripathi, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Both the reviewers are satisfied with the revisions made and suggested the acceptance of the manuscript.

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: All comments have been addressed

Reviewer #2: All comments have been addressed

**********

2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: N/A

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

**********

5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

**********

6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: All the queries are answered and all the suggestions are incorporated in the revised manuscript. It may be accepted for publication in the present form.

Reviewer #2: Revised MS may be accepted for publication on PLOS ONE as it is important for the researcher working in the field of drug resistance.

**********

7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: Yes: Dr. Asimul Islam

Reviewer #2: No

Acceptance letter

Timir Tripathi

16 Jun 2020

PONE-D-20-12977R1

ACD: Antimicrobial chemotherapeutics database

Dear Dr. Khan:

I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department.

If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org.

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on behalf of

Dr. Timir Tripathi

Academic Editor

PLOS ONE

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