Santhi Natchimuthu | Avinashilingam Deemed University for Women (original) (raw)

Papers by Santhi Natchimuthu

International journal of pharma and bio sciences, Oct 11, 2018

Bioinformation, Aug 20, 2011

A crucial virulence factor for intracellular Mycobacterium tuberculosis survival is Protein kinas... more A crucial virulence factor for intracellular Mycobacterium tuberculosis survival is Protein kinase G (PknG), a eukaryotic-like serinethreonine protein kinase expressed by pathogenic mycobacteria that blocks the intracellular degradation of mycobacteria in lysosomes. Inhibition of PknG results in mycobacterial transfer to lysosomes. Withania somnifera, a reputed herb in ayurvedic medicine, comprises a large number of steroidal lactones known as withanolides which show various pharmacological activities. We describe the docking of 26 withanferin and 14 withanolides from Withania somnifera into the three dimensional structure of PknG of M. tuberculosis using GLIDE. The inhibitor binding positions and affinity were evaluated using scoring functions-Glidescore. The withanolide E, F and D and Withaferin-diacetate 2 phenoxy ethyl carbonate were identified as potential inhibitors of PknG. The available drug molecules and the ligand AX20017 showed hydrogen bond interaction with the aminoacid residues Glu233 and Val235. In addition to Val235 the other amino acids, Gly237, Gln238 and Ser239 are important for withanolide inhibitor recognition via hydrogen bonding mechanisms. BIOINFORMATION

Bioinformatics and Biology Insights, 2013

A good understanding of the population dynamics of algal communities is crucial in several ecolog... more A good understanding of the population dynamics of algal communities is crucial in several ecological and pollution studies of freshwater and oceanic systems. This paper reviews the subsequent introduction to the automatic identification of the algal communities using image processing techniques from microscope images. The diverse techniques of image preprocessing, segmentation, feature extraction and recognition are considered one by one and their parameters are summarized. Automatic identification and classification of algal community are very difficult due to various factors such as change in size and shape with climatic changes, various growth periods, and the presence of other microbes. Therefore, the significance, uniqueness, and various approaches are discussed and the analyses in image processing methods are evaluated. Algal identification and associated problems in water organisms have been projected as challenges in image processing application. Various image processing approaches based on textures, shapes, and an object boundary, as well as some segmentation methods like, edge detection and color segmentations, are highlighted. Finally, artificial neural networks and some machine learning algorithms were used to classify and identifying the algae. Further, some of the benefits and drawbacks of schemes are examined.

International Microbiology, Feb 21, 2023

The Indian journal of nutrition and dietetics, Jul 13, 2022

Plants are a valuable source of a multitude of secondary metabolites which have been used as medi... more Plants are a valuable source of a multitude of secondary metabolites which have been used as medicine since times. Most unarguable merit of using plants as a source of medicine is that they are low priced and readily available with very minimal side effects. The present study deals with the comparative analysis of dry and fresh aqueous, ethanolic and chloroform extracts of Rosa indica petals for its phytochemical screening. The results confirmed the presence of almost all tested secondary metabolites in aqueous and ethanolic extracts, whereas chloroform extract showed only the presence of saponins. Further study was proceeded only with dry and fresh aqueous and ethanolic extracts of Rosa indica petals for its antimicrobial activity against Gram negative bacteria including Escherichia coli (ATCC NO: 25922), Pseudomonas aeruginosa (ATCC NO: 27853) and gram positive bacteria including Staphylococcus aureus (ATCC NO: 43300), Enterococcus faecalis (ATCC NO: 29212) and Candida albicans (ATCC NO: 24433) which is an opportunistic pathogenic yeast. Both dry and fresh ethanolic extracts showed a comparatively higher zone of inhibition for all the microbes. Aqueous dry and fresh extracts showed zone of inhibition for Staphylococcus aureus and Enterococcus faecalis, where as none of the extracts showed antimicrobial activity against Candida albicans. Results from the above study suggest that the ethanolic extract of Rosa indica petal are an encouraging alternative to some of the antibacterial drugs. This in turn would potentially be used as natural source to treat various multi drug resistant bacterial strains.

Social Science Research Network, Jan 10, 2020

Bioinformation, Mar 19, 2014

Janus kinase 3 (JAK3) is a non-receptor tyrosine kinases family of protein which is comprised of ... more Janus kinase 3 (JAK3) is a non-receptor tyrosine kinases family of protein which is comprised of JAK1, JAK2, JAK3 and TYK2. It plays an important role in immune function and lymphoid development and it only resides in the hematopoietic system. Therefore, selective targeting JAK3 is a rational approach in developing new therapeutic molecule. In this study, about 116 JAK3 inhibitors were collected from the literature and were used to build four-point pharmacophore model using Phase (Schrodinger module). The statistically significant pharmacophore hypothesis of AAHR.92 with r 2 value of 0.942 was used as 3D query to search against 3D database namely Zincpharmer. A total of 2, 27,483 compounds obtained as hit were subjected to high throughput virtual screening (HTVS module of Schrodinger). Among the hits, ten compounds with good G-score ranging from-12.96 to-11.18 with good binding energy to JAK3 were identified.

The Indian Journal of Nutrition and Dietetics

Plants are a valuable source of a multitude of secondary metabolites which have been used as medi... more Plants are a valuable source of a multitude of secondary metabolites which have been used as medicine since times. Most unarguable merit of using plants as a source of medicine is that they are low priced and readily available with very minimal side effects. The present study deals with the comparative analysis of dry and fresh aqueous, ethanolic and chloroform extracts of Rosa indica petals for its phytochemical screening. The results confirmed the presence of almost all tested secondary metabolites in aqueous and ethanolic extracts, whereas chloroform extract showed only the presence of saponins. Further study was proceeded only with dry and fresh aqueous and ethanolic extracts of Rosa indica petals for its antimicrobial activity against Gram negative bacteria including Escherichia coli (ATCC NO: 25922), Pseudomonas aeruginosa (ATCC NO: 27853) and gram positive bacteria including Staphylococcus aureus (ATCC NO: 43300), Enterococcus faecalis (ATCC NO: 29212) and Candida albicans (A...

Journal of Biomolecular Structure and Dynamics

Biologics

Microbes are hardly seen as planktonic species and are most commonly found as biofilm communities... more Microbes are hardly seen as planktonic species and are most commonly found as biofilm communities in cases of chronic infections. Biofilms are regarded as a biological condition, where a large group of microorganisms gets adhered to a biotic or abiotic surface. In this context, Pseudomonas aeruginosa, a Gram-negative nosocomial pathogen is the main causative organism responsible for life-threatening and persistent infections in individuals affected with cystic fibrosis and other lung ailments. The bacteria can form a strong biofilm structure when it adheres to a surface suitable for the development of a biofilm matrix. These bacterial biofilms pose higher natural resistance to conventional antibiotic therapy due to their multiple tolerance mechanisms. This prevailing condition has led to an increasing rate of treatment failures associated with P. aeruginosa biofilm infections. A better understanding of the effect of a diverse group of antibiotics on established biofilms would be nec...

Bioinformatics and Biology Insights, 2013

A good understanding of the population dynamics of algal communities is crucial in several ecolog... more A good understanding of the population dynamics of algal communities is crucial in several ecological and pollution studies of freshwater and oceanic systems. This paper reviews the subsequent introduction to the automatic identification of the algal communities using image processing techniques from microscope images. The diverse techniques of image preprocessing, segmentation, feature extraction and recognition are considered one by one and their parameters are summarized. Automatic identification and classification of algal community are very difficult due to various factors such as change in size and shape with climatic changes, various growth periods, and the presence of other microbes. Therefore, the significance, uniqueness, and various approaches are discussed and the analyses in image processing methods are evaluated. Algal identification and associated problems in water organisms have been projected as challenges in image processing application. Various image processing approaches based on textures, shapes, and an object boundary, as well as some segmentation methods like, edge detection and color segmentations, are highlighted. Finally, artificial neural networks and some machine learning algorithms were used to classify and identifying the algae. Further, some of the benefits and drawbacks of schemes are examined.

ACS Omega

Pseudomonas aeruginosa, an opportunistic human pathogen, causes fatal effects in patients with cy... more Pseudomonas aeruginosa, an opportunistic human pathogen, causes fatal effects in patients with cystic fibrosis and immunocompromised individuals and leads to around 1000 deaths annually. The quorum sensing mechanism of P. aeruginosa plays a major role in promoting biofilm formation and expression of virulent genes. Hence, quorum sensing inhibition is a promising novel approach to treat these bacterial infections as these organisms show a wide range of antibiotic resistance. Among the interconnected quorum sensing network of P. aeruginosa, targeting the las system is of increased interest as its principal receptor protein LasR is the earliest activated gene. It is also shown to be involved in the regulation of other virulence-associated genes. In this study, we have applied high-throughput virtual screening, an in silico computational method to identify a new class of LasR inhibitors that could serve as potent antagonists to treat P. aeruginosa-associated infections. Three-tire structure-based virtual screening was performed on the Schrodinger small molecule database, which resulted in 12 top hit compounds with docking scores lesser than −11.0 kcal/mol. Three of these best-scored compounds CACPD2011a-0001928786 (C1), CACPD2011a-0001927437 (C2), and CACPD2011a-0000896051 (C3) were further analyzed. The binding free energies of these compounds in complex with the target protein LasR (3IX4) were evaluated, and the pharmacokinetic properties were determined. The stability of the docked complexes was assessed by running a molecular dynamics simulation for 100 ns. Molecular dynamics simulation analysis revealed that all three compounds were found to be in stable contact with the protein over the entire simulation period. The antagonistic effect of these compounds was validated using the LasR reporter gene assay in the presence of acyl homoserine lactone. Significant reduction in the β-galactosidase enzyme activity was achieved at 100 nM concentration for all three compounds pursued. Hence, the present study provides strong evidence that these three compounds could serve as quorum sensing inhibitors of P. aeruginosa LasR protein and can be a probable candidate to treat Pseudomonas-associated infections.

Bioinformation, Jan 1, 2011

A crucial virulence factor for intracellular Mycobacterium tuberculosis survival is Protein kinas... more A crucial virulence factor for intracellular Mycobacterium tuberculosis survival is Protein kinase G (PknG), a eukaryotic-like serinethreonine protein kinase expressed by pathogenic mycobacteria that blocks the intracellular degradation of mycobacteria in lysosomes. Inhibition of PknG results in mycobacterial transfer to lysosomes. Withania somnifera, a reputed herb in ayurvedic medicine, comprises a large number of steroidal lactones known as withanolides which show various pharmacological activities. We describe the docking of 26 withanferin and 14 withanolides from Withania somnifera into the three dimensional structure of PknG of M. tuberculosis using GLIDE. The inhibitor binding positions and affinity were evaluated using scoring functions- Glidescore. The withanolide E, F and D and Withaferin - diacetate 2 phenoxy ethyl carbonate were identified as potential inhibitors of PknG. The available drug molecules and the ligand AX20017 showed hydrogen bond interaction with the aminoacid residues Glu233 and Val235. In addition to Val235 the other amino acids, Gly237, Gln238 and Ser239 are important for withanolide inhibitor recognition via hydrogen bonding mechanisms.

International journal of pharma and bio sciences, Oct 11, 2018

Bioinformation, Aug 20, 2011

A crucial virulence factor for intracellular Mycobacterium tuberculosis survival is Protein kinas... more A crucial virulence factor for intracellular Mycobacterium tuberculosis survival is Protein kinase G (PknG), a eukaryotic-like serinethreonine protein kinase expressed by pathogenic mycobacteria that blocks the intracellular degradation of mycobacteria in lysosomes. Inhibition of PknG results in mycobacterial transfer to lysosomes. Withania somnifera, a reputed herb in ayurvedic medicine, comprises a large number of steroidal lactones known as withanolides which show various pharmacological activities. We describe the docking of 26 withanferin and 14 withanolides from Withania somnifera into the three dimensional structure of PknG of M. tuberculosis using GLIDE. The inhibitor binding positions and affinity were evaluated using scoring functions-Glidescore. The withanolide E, F and D and Withaferin-diacetate 2 phenoxy ethyl carbonate were identified as potential inhibitors of PknG. The available drug molecules and the ligand AX20017 showed hydrogen bond interaction with the aminoacid residues Glu233 and Val235. In addition to Val235 the other amino acids, Gly237, Gln238 and Ser239 are important for withanolide inhibitor recognition via hydrogen bonding mechanisms. BIOINFORMATION

Bioinformatics and Biology Insights, 2013

A good understanding of the population dynamics of algal communities is crucial in several ecolog... more A good understanding of the population dynamics of algal communities is crucial in several ecological and pollution studies of freshwater and oceanic systems. This paper reviews the subsequent introduction to the automatic identification of the algal communities using image processing techniques from microscope images. The diverse techniques of image preprocessing, segmentation, feature extraction and recognition are considered one by one and their parameters are summarized. Automatic identification and classification of algal community are very difficult due to various factors such as change in size and shape with climatic changes, various growth periods, and the presence of other microbes. Therefore, the significance, uniqueness, and various approaches are discussed and the analyses in image processing methods are evaluated. Algal identification and associated problems in water organisms have been projected as challenges in image processing application. Various image processing approaches based on textures, shapes, and an object boundary, as well as some segmentation methods like, edge detection and color segmentations, are highlighted. Finally, artificial neural networks and some machine learning algorithms were used to classify and identifying the algae. Further, some of the benefits and drawbacks of schemes are examined.

International Microbiology, Feb 21, 2023

The Indian journal of nutrition and dietetics, Jul 13, 2022

Plants are a valuable source of a multitude of secondary metabolites which have been used as medi... more Plants are a valuable source of a multitude of secondary metabolites which have been used as medicine since times. Most unarguable merit of using plants as a source of medicine is that they are low priced and readily available with very minimal side effects. The present study deals with the comparative analysis of dry and fresh aqueous, ethanolic and chloroform extracts of Rosa indica petals for its phytochemical screening. The results confirmed the presence of almost all tested secondary metabolites in aqueous and ethanolic extracts, whereas chloroform extract showed only the presence of saponins. Further study was proceeded only with dry and fresh aqueous and ethanolic extracts of Rosa indica petals for its antimicrobial activity against Gram negative bacteria including Escherichia coli (ATCC NO: 25922), Pseudomonas aeruginosa (ATCC NO: 27853) and gram positive bacteria including Staphylococcus aureus (ATCC NO: 43300), Enterococcus faecalis (ATCC NO: 29212) and Candida albicans (ATCC NO: 24433) which is an opportunistic pathogenic yeast. Both dry and fresh ethanolic extracts showed a comparatively higher zone of inhibition for all the microbes. Aqueous dry and fresh extracts showed zone of inhibition for Staphylococcus aureus and Enterococcus faecalis, where as none of the extracts showed antimicrobial activity against Candida albicans. Results from the above study suggest that the ethanolic extract of Rosa indica petal are an encouraging alternative to some of the antibacterial drugs. This in turn would potentially be used as natural source to treat various multi drug resistant bacterial strains.

Social Science Research Network, Jan 10, 2020

Bioinformation, Mar 19, 2014

Janus kinase 3 (JAK3) is a non-receptor tyrosine kinases family of protein which is comprised of ... more Janus kinase 3 (JAK3) is a non-receptor tyrosine kinases family of protein which is comprised of JAK1, JAK2, JAK3 and TYK2. It plays an important role in immune function and lymphoid development and it only resides in the hematopoietic system. Therefore, selective targeting JAK3 is a rational approach in developing new therapeutic molecule. In this study, about 116 JAK3 inhibitors were collected from the literature and were used to build four-point pharmacophore model using Phase (Schrodinger module). The statistically significant pharmacophore hypothesis of AAHR.92 with r 2 value of 0.942 was used as 3D query to search against 3D database namely Zincpharmer. A total of 2, 27,483 compounds obtained as hit were subjected to high throughput virtual screening (HTVS module of Schrodinger). Among the hits, ten compounds with good G-score ranging from-12.96 to-11.18 with good binding energy to JAK3 were identified.

The Indian Journal of Nutrition and Dietetics

Plants are a valuable source of a multitude of secondary metabolites which have been used as medi... more Plants are a valuable source of a multitude of secondary metabolites which have been used as medicine since times. Most unarguable merit of using plants as a source of medicine is that they are low priced and readily available with very minimal side effects. The present study deals with the comparative analysis of dry and fresh aqueous, ethanolic and chloroform extracts of Rosa indica petals for its phytochemical screening. The results confirmed the presence of almost all tested secondary metabolites in aqueous and ethanolic extracts, whereas chloroform extract showed only the presence of saponins. Further study was proceeded only with dry and fresh aqueous and ethanolic extracts of Rosa indica petals for its antimicrobial activity against Gram negative bacteria including Escherichia coli (ATCC NO: 25922), Pseudomonas aeruginosa (ATCC NO: 27853) and gram positive bacteria including Staphylococcus aureus (ATCC NO: 43300), Enterococcus faecalis (ATCC NO: 29212) and Candida albicans (A...

Journal of Biomolecular Structure and Dynamics

Biologics

Microbes are hardly seen as planktonic species and are most commonly found as biofilm communities... more Microbes are hardly seen as planktonic species and are most commonly found as biofilm communities in cases of chronic infections. Biofilms are regarded as a biological condition, where a large group of microorganisms gets adhered to a biotic or abiotic surface. In this context, Pseudomonas aeruginosa, a Gram-negative nosocomial pathogen is the main causative organism responsible for life-threatening and persistent infections in individuals affected with cystic fibrosis and other lung ailments. The bacteria can form a strong biofilm structure when it adheres to a surface suitable for the development of a biofilm matrix. These bacterial biofilms pose higher natural resistance to conventional antibiotic therapy due to their multiple tolerance mechanisms. This prevailing condition has led to an increasing rate of treatment failures associated with P. aeruginosa biofilm infections. A better understanding of the effect of a diverse group of antibiotics on established biofilms would be nec...

Bioinformatics and Biology Insights, 2013

A good understanding of the population dynamics of algal communities is crucial in several ecolog... more A good understanding of the population dynamics of algal communities is crucial in several ecological and pollution studies of freshwater and oceanic systems. This paper reviews the subsequent introduction to the automatic identification of the algal communities using image processing techniques from microscope images. The diverse techniques of image preprocessing, segmentation, feature extraction and recognition are considered one by one and their parameters are summarized. Automatic identification and classification of algal community are very difficult due to various factors such as change in size and shape with climatic changes, various growth periods, and the presence of other microbes. Therefore, the significance, uniqueness, and various approaches are discussed and the analyses in image processing methods are evaluated. Algal identification and associated problems in water organisms have been projected as challenges in image processing application. Various image processing approaches based on textures, shapes, and an object boundary, as well as some segmentation methods like, edge detection and color segmentations, are highlighted. Finally, artificial neural networks and some machine learning algorithms were used to classify and identifying the algae. Further, some of the benefits and drawbacks of schemes are examined.

ACS Omega

Pseudomonas aeruginosa, an opportunistic human pathogen, causes fatal effects in patients with cy... more Pseudomonas aeruginosa, an opportunistic human pathogen, causes fatal effects in patients with cystic fibrosis and immunocompromised individuals and leads to around 1000 deaths annually. The quorum sensing mechanism of P. aeruginosa plays a major role in promoting biofilm formation and expression of virulent genes. Hence, quorum sensing inhibition is a promising novel approach to treat these bacterial infections as these organisms show a wide range of antibiotic resistance. Among the interconnected quorum sensing network of P. aeruginosa, targeting the las system is of increased interest as its principal receptor protein LasR is the earliest activated gene. It is also shown to be involved in the regulation of other virulence-associated genes. In this study, we have applied high-throughput virtual screening, an in silico computational method to identify a new class of LasR inhibitors that could serve as potent antagonists to treat P. aeruginosa-associated infections. Three-tire structure-based virtual screening was performed on the Schrodinger small molecule database, which resulted in 12 top hit compounds with docking scores lesser than −11.0 kcal/mol. Three of these best-scored compounds CACPD2011a-0001928786 (C1), CACPD2011a-0001927437 (C2), and CACPD2011a-0000896051 (C3) were further analyzed. The binding free energies of these compounds in complex with the target protein LasR (3IX4) were evaluated, and the pharmacokinetic properties were determined. The stability of the docked complexes was assessed by running a molecular dynamics simulation for 100 ns. Molecular dynamics simulation analysis revealed that all three compounds were found to be in stable contact with the protein over the entire simulation period. The antagonistic effect of these compounds was validated using the LasR reporter gene assay in the presence of acyl homoserine lactone. Significant reduction in the β-galactosidase enzyme activity was achieved at 100 nM concentration for all three compounds pursued. Hence, the present study provides strong evidence that these three compounds could serve as quorum sensing inhibitors of P. aeruginosa LasR protein and can be a probable candidate to treat Pseudomonas-associated infections.

Bioinformation, Jan 1, 2011

A crucial virulence factor for intracellular Mycobacterium tuberculosis survival is Protein kinas... more A crucial virulence factor for intracellular Mycobacterium tuberculosis survival is Protein kinase G (PknG), a eukaryotic-like serinethreonine protein kinase expressed by pathogenic mycobacteria that blocks the intracellular degradation of mycobacteria in lysosomes. Inhibition of PknG results in mycobacterial transfer to lysosomes. Withania somnifera, a reputed herb in ayurvedic medicine, comprises a large number of steroidal lactones known as withanolides which show various pharmacological activities. We describe the docking of 26 withanferin and 14 withanolides from Withania somnifera into the three dimensional structure of PknG of M. tuberculosis using GLIDE. The inhibitor binding positions and affinity were evaluated using scoring functions- Glidescore. The withanolide E, F and D and Withaferin - diacetate 2 phenoxy ethyl carbonate were identified as potential inhibitors of PknG. The available drug molecules and the ligand AX20017 showed hydrogen bond interaction with the aminoacid residues Glu233 and Val235. In addition to Val235 the other amino acids, Gly237, Gln238 and Ser239 are important for withanolide inhibitor recognition via hydrogen bonding mechanisms.