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Article ; Online: A drug repurposing endeavor to discover a multi-targeting ligand against RhlR and LasR proteins from opportunistic human pathogen Pseudomonas aeruginosa.

Chowdhury, Nilkanta / Bagchi, Angshuman

2022 Volume 28, Issue 10, Page(s) 295

Abstract: Pseudomonas aeruginosa is an opportunistic human pathogen. It synthesizes the poison called Hydrogen Cyanide (HCN). The synthesis of HCN is mediated by the enzyme HCN synthase which is obtained from the hcnABC operon and the transcription of the hcnABC ... ...

Abstract	Pseudomonas aeruginosa is an opportunistic human pathogen. It synthesizes the poison called Hydrogen Cyanide (HCN). The synthesis of HCN is mediated by the enzyme HCN synthase which is obtained from the hcnABC operon and the transcription of the hcnABC operon is mediated by three proteins LasR, RhlR, and ANR. In our previous works, we analyzed the activation process of RhlR and LasR proteins by their cognate auto-inducer ligands (N-butanoyl-L-homoserine lactone and N-(3-oxododecanoyl)-homoserine lactone respectively). In this work, we attempted to identify some multi-targeting ligands which would be able to destroy the structural integrity of both the RhlR and LasR proteins using steered MD simulations. We used the virtual screening of ligand libraries, and for that purpose, we used the NCI drug database. We selected the top 4 ligands from our virtual screening experiments. We then tried to check their relative binding affinities with the LasR and RhlR proteins in comparison to their native auto-inducer ligands. Through this work, we were able to identify 4 such ligands which were capable of binding to both the RhlR and LasR proteins in a better way than their native auto-inducer ligands. The efficacies of these ligands to actually perturb the structural integrity of RhlR and LasR proteins could be tested in wet lab. The work is the first work in the field of structure-based drug design to come up with possible multi-targeting drug-like structures against the RhlR and LasR proteins from Pseudomonas aeruginosa.
MeSH term(s)	Bacterial Proteins/metabolism ; Drug Repositioning ; Humans ; Ligands ; Pseudomonas aeruginosa/metabolism ; Trans-Activators/metabolism
Chemical Substances	Bacterial Proteins ; Ligands ; Trans-Activators
Language	English
Publishing date	2022-09-05
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1284729-X
ISSN	0948-5023 ; 1610-2940
ISSN (online)	0948-5023
ISSN	1610-2940
DOI	10.1007/s00894-022-05301-w
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Article ; Online: A drug repurposing endeavor to discover a multi-targeting ligand against RhlR and LasR proteins from opportunistic human pathogen Pseudomonas aeruginosa

Chowdhury, Nilkanta / Bagchi, Angshuman

J issuedModel. 2022 Oct., v. 28, no. 10, p. 295

2022 , Page(s) 295

Abstract	Pseudomonas aeruginosa is an opportunistic human pathogen. It synthesizes the poison called Hydrogen Cyanide (HCN). The synthesis of HCN is mediated by the enzyme HCN synthase which is obtained from the hcnABC operon and the transcription of the hcnABC operon is mediated by three proteins LasR, RhlR, and ANR. In our previous works, we analyzed the activation process of RhlR and LasR proteins by their cognate auto-inducer ligands (N-butanoyl-L-homoserine lactone and N-(3-oxododecanoyl)-homoserine lactone respectively). In this work, we attempted to identify some multi-targeting ligands which would be able to destroy the structural integrity of both the RhlR and LasR proteins using steered MD simulations. We used the virtual screening of ligand libraries, and for that purpose, we used the NCI drug database. We selected the top 4 ligands from our virtual screening experiments. We then tried to check their relative binding affinities with the LasR and RhlR proteins in comparison to their native auto-inducer ligands. Through this work, we were able to identify 4 such ligands which were capable of binding to both the RhlR and LasR proteins in a better way than their native auto-inducer ligands. The efficacies of these ligands to actually perturb the structural integrity of RhlR and LasR proteins could be tested in wet lab. The work is the first work in the field of structure-based drug design to come up with possible multi-targeting drug-like structures against the RhlR and LasR proteins from Pseudomonas aeruginosa.
Keywords	Pseudomonas aeruginosa ; animal pathogens ; databases ; drug design ; drugs ; enzymes ; hydrogen cyanide ; ligands ; models ; operon
Language	English
Dates of publication	2022-10
Size	p. 295
Publishing place	Springer Berlin Heidelberg
Document type	Article ; Online
ZDB-ID	1284729-X
ISSN	0948-5023 ; 1610-2940
ISSN (online)	0948-5023
ISSN	1610-2940
DOI	10.1007/s00894-022-05301-w
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Article ; Online: Elucidation of the hetero-dimeric binding activity of LasR and RhlR proteins with the promoter DNA and the role of a specific Phe residue during the biosynthesis of HCN synthase from opportunistic pathogen Pseudomonas aeruginosa.

Chowdhury, Nilkanta / Bagchi, Angshuman

Journal of molecular modeling

2021 Volume 27, Issue 3, Page(s) 76

Abstract: Pseudomonas aeruginosa is an opportunistic human pathogen. It causes secondary infections in patients suffering from cancer and other immunological disorders. The pathogenicity of the organism is dependent on the ability of the organism to code for ... ...

Abstract	Pseudomonas aeruginosa is an opportunistic human pathogen. It causes secondary infections in patients suffering from cancer and other immunological disorders. The pathogenicity of the organism is dependent on the ability of the organism to code for hydrogen cyanide (HCN), the synthesis of which is mediated by HCN synthase enzyme. HCN synthase is encoded by hcnABC operon. The transcription of the operon is controlled by a complex interplay between the proteins LasR and RhlR. Till date, there is no report that deals with the binding interactions of the RhlR-LasR heterodimer with the promoter DNA region of the hcnABC operon. We, for the first time, tried to analyse the binding modes of the RhlR-LasR heterodimer with the promoter DNA regions. From our work, we could predict the importance of a specific amino acid residue Phe214 from RhlR which might be considered to have the desired specificity to bind to the promoter DNA. Therefore, the amino acid Phe214 may be targeted to develop suitable ligands to eradicate the spread of secondary infections by Pseudomonas aeruginosa.
MeSH term(s)	Bacterial Proteins/chemistry ; Bacterial Proteins/metabolism ; Binding Sites ; Hydrogen Cyanide ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Oxidoreductases Acting on CH-NH2 Group Donors/chemistry ; Oxidoreductases Acting on CH-NH2 Group Donors/metabolism ; Promoter Regions, Genetic ; Protein Binding ; Protein Multimerization ; Pseudomonas aeruginosa ; Trans-Activators/chemistry ; Trans-Activators/metabolism
Chemical Substances	Bacterial Proteins ; LasR protein, Pseudomonas aeruginosa ; Trans-Activators ; Hydrogen Cyanide (2WTB3V159F) ; Oxidoreductases Acting on CH-NH2 Group Donors (EC 1.4.-) ; glycine dehydrogenase (cyanide-forming) (EC 1.4.99.5)
Language	English
Publishing date	2021-02-08
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1284729-X
ISSN	0948-5023 ; 1610-2940
ISSN (online)	0948-5023
ISSN	1610-2940
DOI	10.1007/s00894-021-04701-8
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Article ; Online: Identification of the binding interactions of some novel antiviral compounds against Nsp1 protein from SARS-CoV-2 (COVID-19) through high throughput screening.

Chowdhury, Nilkanta / Bagchi, Angshuman

Journal of biomolecular structure & dynamics

2021 Volume 40, Issue 14, Page(s) 6634–6641

Abstract: The SARS-CoV-2 pandemic has become a global threat. It has become very difficult to control the spreading of the virus. The virus is a RNA virus and the virulence of the virus is mediated by three virulence causing proteins, viz., Nsp1, Nsp3c and ORF7. ... ...

Abstract	The SARS-CoV-2 pandemic has become a global threat. It has become very difficult to control the spreading of the virus. The virus is a RNA virus and the virulence of the virus is mediated by three virulence causing proteins, viz., Nsp1, Nsp3c and ORF7. So far the drug designing endeavors against the virus have been being targeted towards the spike protein which is responsible for the entry of the virus inside human host as well as the RNA dependent RNA polymerase. However, no effective treatment against the virus has so far been developed. In the present situation, an attempt has been made to target the virulence protein factor Nsp1 which binds to the 40S ribosomal subunit of the human host. We tried to target the Nsp1 by in-silico virtual screening of ligand libraries. We built the three dimensional structure of Nsp1 and used the structure to screen the ChEMBL drug library. We used molecular docking simulations of the top6 screened ligands with Nsp1 and subjected the liagnd-Nsp1 complexes to molecular dynamics simulations to analyze the behaviors of the ligands in a virtual cell. From our analysis we could predict that the ligands bearing the ChEMBL identifiers, CHEMBL1096281, CHEMBL2022920, CHEMBL175656, had the best binding affinity values with Nsp1. Therefore, these ligand molecules may be tested in wet-lab for further analysis. This is the first report to target the virulence factor Nsp1 from SARS-CoV-2. Communicated by Ramaswamy H. Sarma.
MeSH term(s)	Antiviral Agents/pharmacology ; COVID-19/drug therapy ; High-Throughput Screening Assays ; Humans ; Ligands ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; SARS-CoV-2 ; Viral Nonstructural Proteins/chemistry
Chemical Substances	Antiviral Agents ; Ligands ; Viral Nonstructural Proteins
Language	English
Publishing date	2021-02-22
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2021.1887763
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Article ; Online: Fluorescence probing and molecular docking analysis of the binding interaction of bovine serum albumin (BSA) with the polarity probe AICCN.

Mandal, Barun / Chowdhury, Nilkanta / Baildya, Nabajyoti / Mandal, Ranju Prasad / Bagchi, Angshuman / De, Swati

Physical chemistry chemical physics : PCCP

2023 Volume 25, Issue 27, Page(s) 18197–18214

Abstract: In this work, the fluorescent probe 2-amino-4-( ... ...

Abstract	In this work, the fluorescent probe 2-amino-4-(1
MeSH term(s)	Serum Albumin, Bovine/chemistry ; Molecular Docking Simulation ; Spectrometry, Fluorescence ; Prospective Studies ; Binding Sites ; Fluorescent Dyes/chemistry ; Protein Binding ; Thermodynamics
Chemical Substances	Serum Albumin, Bovine (27432CM55Q) ; Fluorescent Dyes
Language	English
Publishing date	2023-07-12
Publishing country	England
Document type	Journal Article
ZDB-ID	1476244-4
ISSN	1463-9084 ; 1463-9076
ISSN (online)	1463-9084
ISSN	1463-9076
DOI	10.1039/d2cp04124c
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Article: Comparative analysis of prokaryotic and eukaryotic transcription factors using machine-learning techniques.

Nilkanta, Chowdhury / Bagchi, Angshuman

Bioinformation

2018 Volume 14, Issue 6, Page(s) 315–326

Abstract: The DNA-protein interactions play vital roles in the central dogma of molecular biology. Proper interactions between DNA and protein would lead to the onset of various biological phenomena like transcription, translation, and replication. However, the ... ...

Abstract	The DNA-protein interactions play vital roles in the central dogma of molecular biology. Proper interactions between DNA and protein would lead to the onset of various biological phenomena like transcription, translation, and replication. However, the mechanisms of these well-known processes vary between prokaryotic and eukaryotic organisms. The exact molecular mechanisms of these processes are unknown. Therefore, it is of interest to report the comparative estimate of the different properties of the DNA binding proteins from prokaryotic and eukaryotic organisms. We analyzed the different sequence-based features such as the frequency of amino acids and amino acid groups in the proteins of prokaryotes and eukaryotes by statistical measures. The general pattern of differences between the various DNA binding proteins for the development of a prediction system to discriminate between these proteins between prokaryotes and eukaryotes is documented.
Language	English
Publishing date	2018-06-30
Publishing country	Singapore
Document type	Journal Article
ZDB-ID	2203786-X
ISSN	0973-2063
ISSN	0973-2063
DOI	10.6026/97320630014315
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Article ; Online: Structural Characterization of the Hidden Peptide SHPRH-146aa Encoded by Non-Coding circ-SHPRH to Act as Tumor Suppressor.

Biswas, Aniruddha / Chowdhury, Nilkanta / Bagchi, Angshuman

Applied biochemistry and biotechnology

2021 Volume 193, Issue 7, Page(s) 2076–2086

Abstract: Circular RNAs belong to the class of non-coding RNA molecules, though surprisingly some of them have protein-coding potentials. However, the circular RNA circ-SHPRH is known to code for an unusual protein known as SHPRH-146aa. However, the molecular ... ...

Abstract	Circular RNAs belong to the class of non-coding RNA molecules, though surprisingly some of them have protein-coding potentials. However, the circular RNA circ-SHPRH is known to code for an unusual protein known as SHPRH-146aa. However, the molecular level details of the protein are not yet identified. It was proposed that the protein has its role in glioblastoma. Therefore, in this work, an attempt was made to decipher the various structural features of SHPRH-146aa. The binding interactions of the protein SHPRH-146aa with its partner protein DTL were also analyzed. The main aim of the work was to decipher the characteristics features of this unusual protein and the region on SHPRH-146aa that would form different types of non-covalent binding interactions both among itself as well as with its binding partner. In this work, we tried to elucidate the various structural and physico-chemical features of the protein as well as its mode of interactions with its binding partner. The study would therefore pave the pathway to design future wet lab experiments to delineate the appropriate structural features of the protein as well as its association with glioblastoma and neuro-degenerative diseases.
MeSH term(s)	DNA Helicases/chemistry ; DNA Helicases/genetics ; Humans ; Peptides/chemistry ; Peptides/genetics ; Protein Structure, Secondary ; RNA, Circular/genetics ; Tumor Suppressor Proteins/chemistry ; Tumor Suppressor Proteins/genetics ; Ubiquitin-Protein Ligases/chemistry ; Ubiquitin-Protein Ligases/genetics
Chemical Substances	Peptides ; RNA, Circular ; Tumor Suppressor Proteins ; SHPRH protein, human (EC 2.3.2.27) ; Ubiquitin-Protein Ligases (EC 2.3.2.27) ; DNA Helicases (EC 3.6.4.-)
Language	English
Publishing date	2021-02-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	392344-7
ISSN	1559-0291 ; 0273-2289
ISSN (online)	1559-0291
ISSN	0273-2289
DOI	10.1007/s12010-021-03520-0
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Article: Structural Characterization of the Hidden Peptide SHPRH-146aa Encoded by Non-Coding circ-SHPRH to Act as Tumor Suppressor

Biswas, Aniruddha / Chowdhury, Nilkanta / Bagchi, Angshuman

Applied biochemistry and biotechnology. 2021 July, v. 193, no. 7

2021

Abstract	Circular RNAs belong to the class of non-coding RNA molecules, though surprisingly some of them have protein-coding potentials. However, the circular RNA circ-SHPRH is known to code for an unusual protein known as SHPRH-146aa. However, the molecular level details of the protein are not yet identified. It was proposed that the protein has its role in glioblastoma. Therefore, in this work, an attempt was made to decipher the various structural features of SHPRH-146aa. The binding interactions of the protein SHPRH-146aa with its partner protein DTL were also analyzed. The main aim of the work was to decipher the characteristics features of this unusual protein and the region on SHPRH-146aa that would form different types of non-covalent binding interactions both among itself as well as with its binding partner. In this work, we tried to elucidate the various structural and physico-chemical features of the protein as well as its mode of interactions with its binding partner. The study would therefore pave the pathway to design future wet lab experiments to delineate the appropriate structural features of the protein as well as its association with glioblastoma and neuro-degenerative diseases.
Keywords	biotechnology ; circular RNA ; glioblastoma ; non-coding RNA ; peptides
Language	English
Dates of publication	2021-07
Size	p. 2076-2086.
Publishing place	Springer US
Document type	Article
ZDB-ID	392344-7
ISSN	0273-2289
ISSN	0273-2289
DOI	10.1007/s12010-021-03520-0
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Article ; Online: Omeprazole prevents stress induced gastric ulcer by direct inhibition of MMP-2/TIMP-3 interactions.

Rudra, Deep Sankar / Pal, Uttam / Chowdhury, Nilkanta / Maiti, Nakul Chandra / Bagchi, Angshuman / Swarnakar, Snehasikta

Free radical biology & medicine

2022 Volume 181, Page(s) 221–234

Abstract: The healing of damaged tissues in gastric tract starts with the extracellular matrix (ECM) remodeling by the action of matrix metalloproteinases (MMPs). Particularly, MMP-2 (gelatinase-A) maintains ECM structure and function by degrading type IV collagen, ...

Abstract	The healing of damaged tissues in gastric tract starts with the extracellular matrix (ECM) remodeling by the action of matrix metalloproteinases (MMPs). Particularly, MMP-2 (gelatinase-A) maintains ECM structure and function by degrading type IV collagen, the major component of basement membranes and by clearing denatured collagen. The proteolytic activities of MMPs are critically balanced by endogenous tissue inhibitors of metalloproteinases (TIMPs) and disruption of this balance results in several diseases. The well-known drug omeprazole is a proton pump inhibitor used for curing gastric ulcer. However, the action of omeprazole in ECM remodeling on gastroprotection has never been explored. Herein, using rat model of gastric ulcer, we report that restraint cold stress caused increase apoptosis to surface epithelia of gastric tissues along with TIMP-3 upregulation and inhibition of MMP-2 activity thereon. In contrast, omeprazole treatment suppressed TIMP-3 while increasing MMP-2 activity and thereby, restoring MMP-2/TIMP-3 balance. Additionally, nanomolar binding constant (K
MeSH term(s)	Animals ; Matrix Metalloproteinase 2/genetics ; Matrix Metalloproteinase 2/metabolism ; Omeprazole/pharmacology ; Rats ; Stomach Ulcer/drug therapy ; Stomach Ulcer/metabolism ; Stomach Ulcer/prevention & control ; Tissue Inhibitor of Metalloproteinase-3/genetics ; Tissue Inhibitor of Metalloproteinase-3/metabolism ; Tissue Inhibitor of Metalloproteinases/metabolism
Chemical Substances	Tissue Inhibitor of Metalloproteinase-3 ; Tissue Inhibitor of Metalloproteinases ; Matrix Metalloproteinase 2 (EC 3.4.24.24) ; Omeprazole (KG60484QX9)
Language	English
Publishing date	2022-02-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	807032-5
ISSN	1873-4596 ; 0891-5849
ISSN (online)	1873-4596
ISSN	0891-5849
DOI	10.1016/j.freeradbiomed.2022.02.007
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Article ; Online: Identification of ligand binding activity and DNA recognition by RhlR protein from opportunistic pathogen Pseudomonas aeruginosa-a molecular dynamic simulation approach.

Chowdhury, Nilkanta / Bagchi, Angshuman

Journal of molecular recognition : JMR

2018 Volume 31, Issue 12, Page(s) e2738

Abstract: RhlR protein from opportunistic pathogen Pseudomonas aeruginosa is involved in the transcription of virulence genes of the organism. The RhlR protein functions as a dimer and binds to the cognate promoter DNA with the help of an autoinducer ligand BHL to ...

Abstract	RhlR protein from opportunistic pathogen Pseudomonas aeruginosa is involved in the transcription of virulence genes of the organism. The RhlR protein functions as a dimer and binds to the cognate promoter DNA with the help of an autoinducer ligand BHL to initiate the transcription of the virulence genes. Till date, there are no reports that detail the mechanism of virulence gene expression by RhlR protein in P. aeruginosa. In this work, we tried to analyse the molecular aspects of the various binding interactions of the RhlR protein while formimg the dimmer as well as with the promoter DNA. We analysed the mode of dimerisation of the RhlR protein and its binding interactions with the autoinducer BHL ligand. From our analyses, we could identify the potential amino acid residues which are involved in the binding interactions. We also predicted how the autoinducer BHL would help in making contacts with the DNA as well as with itself. Thus, the autoinducer BHL would serve as an important mediator of molecular interactions involved in binding the RhlR protein to itself as well as with the promoter DNA. Therefore, any other molecule which would be able to compete with the autoinducer ligand BHL to bind to RhlR protein but would not let the RhlR protein bind the promoter DNA would be an ideal drug candidate to prevent the transcription process of the virulence genes in P. aeruginosa. Our future aim is to predict suitable ligands which would compete with BHL to thwart the transcription process.
MeSH term(s)	4-Butyrolactone/analogs & derivatives ; 4-Butyrolactone/metabolism ; Bacterial Proteins/chemistry ; Bacterial Proteins/metabolism ; Binding Sites ; DNA, Bacterial/genetics ; DNA, Bacterial/metabolism ; Gene Expression Regulation, Bacterial ; Ligands ; Models, Molecular ; Molecular Dynamics Simulation ; Promoter Regions, Genetic ; Protein Binding ; Protein Multimerization ; Pseudomonas aeruginosa/genetics ; Pseudomonas aeruginosa/metabolism ; Transcription, Genetic
Chemical Substances	Bacterial Proteins ; DNA, Bacterial ; Ligands ; N-butyrylhomoserine lactone ; RhlR protein, Pseudomonas aeruginosa ; homoserine lactone (1192-20-7) ; 4-Butyrolactone (OL659KIY4X)
Language	English
Publishing date	2018-07-02
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1015084-5
ISSN	1099-1352 ; 0952-3499
ISSN (online)	1099-1352
ISSN	0952-3499
DOI	10.1002/jmr.2738
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