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Article: Could Dermaseptin Analogue be a Competitive Inhibitor for ACE2 Towards Binding with Viral Spike Protein Causing COVID19?: Computational Investigation.

Sekar, P Chandra / Rajasekaran, R

International journal of peptide research and therapeutics

2021 Volume 27, Issue 2, Page(s) 1043–1056

Abstract: Initial phase of COVID-19 infection is associated with the binding of viral spike protein S1 receptor binding domain (RBD) with the host cell surface receptor, ACE2. Peptide inhibitors typically interact with spike proteins in order to block its ... ...

Abstract	Initial phase of COVID-19 infection is associated with the binding of viral spike protein S1 receptor binding domain (RBD) with the host cell surface receptor, ACE2. Peptide inhibitors typically interact with spike proteins in order to block its interaction with ACE2, and this knowledge would promote the use of such peptides as therapeutic scaffolds. The present study examined the competitive inhibitor activity of a broad spectrum antimicrobial peptide, Dermaseptin-S4 (S4) and its analogues. Three structural S4 analogues viz., S4 (K
Language	English
Publishing date	2021-01-16
Publishing country	United States
Document type	Journal Article
ZDB-ID	2192632-3
ISSN	1573-3904 ; 1573-3149
ISSN (online)	1573-3904
ISSN	1573-3149
DOI	10.1007/s10989-020-10149-w
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Article ; Online: Impact of monsoon season rainfall spells on the ecosystem carbon exchanges of Himalayan Chir-Pine and Banj-Oak-dominated forests: a comparative assessment.

Lohani, Priyanka / Mukherjee, Sandipan / Sekar, K Chandra / Mehta, Pooja / Kumar, Kireet / Dimri, A P

Environmental monitoring and assessment

2023 Volume 195, Issue 7, Page(s) 827

Abstract: The Chir-Pine (Pinus roxburghii) and Banj-Oak (Quercus leucotrichophora)-dominated ecosystems of central Himalaya provide significant green services. However, responses of these ecosystems, with respect to ecosystem carbon flux variability, to changing ... ...

Abstract	The Chir-Pine (Pinus roxburghii) and Banj-Oak (Quercus leucotrichophora)-dominated ecosystems of central Himalaya provide significant green services. However, responses of these ecosystems, with respect to ecosystem carbon flux variability, to changing microclimate are not yet studied. Since quantification of ecosystem responses to fluctuation in the microclimate, particularly rainfall, is expected to be beneficial for management of these ecosystems, this study aims (i) to quantify and compare amplitude of rainfall-induced change in the carbon fluxes of Chir-Pine and Banj-Oak-dominated ecosystems using wavelet methods, and (ii) to quantify and compare dissimilarities in the ecosystem exchanges due to varying rainfall spell and amount. Eddy covariance-based continuous daily micrometeorological and flux data, during the 2016-2017 monsoon seasons (total 244 days, 122 days of June-September), from two sites in Uttarakhand, India, are used for this purpose. We find that both Chir-Pine and Banj-Oak-dominated ecosystems are the sinks of carbon, and Chir-Pine-dominated ecosystem sequesters around 1.8 times higher carbon than the Banj-Oak. A systematic enhancement in the carbon assimilation of the Chir-Pine-dominated ecosystem is noted with increasing rainfall spell following a statistically significant power-law relationship. We have also identified a rainfall amount threshold for Chir-Pine and Banj-Oak-dominated ecosystems (10 ± 0.7 and 17 ± 1.2 mm, respectively) that resulted in highest ecosystem carbon assimilation in monsoon. The general inference of this study accentuates that Banj-Oak-dominated ecosystem is more sensitive to maximum rain within a spell whereas the Chir-Pine-dominated ecosystem is more responsive to increasing rainfall spell duration.
MeSH term(s)	Ecosystem ; Quercus/physiology ; Seasons ; Carbon ; Trees/physiology ; Environmental Monitoring ; Forests ; Pinus
Chemical Substances	Carbon (7440-44-0)
Language	English
Publishing date	2023-06-09
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	782621-7
ISSN	1573-2959 ; 0167-6369
ISSN (online)	1573-2959
ISSN	0167-6369
DOI	10.1007/s10661-023-11297-4
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Article ; Online: Molecular simulation unravels the amyloidogenic misfolding of nascent ApoA1 protein, driven by deleterious point mutations occurring in between 170-178 hotspot region.

Chandrasekhar, G / Chandra Sekar, P / Srinivasan, E / Amarnath, A / Pengyong, H / Rajasekaran, R

Journal of biomolecular structure & dynamics

2021 Volume 40, Issue 23, Page(s) 13278–13290

Abstract: Protein ApoA1 is extensively studied for its role in lipid metabolism. Its seedy dark side of amyloid formulation remains relatively understudied yet. Due to genetic mutations, the protein pathologically misshapes into its amyloid form that gets ... ...

Abstract	Protein ApoA1 is extensively studied for its role in lipid metabolism. Its seedy dark side of amyloid formulation remains relatively understudied yet. Due to genetic mutations, the protein pathologically misshapes into its amyloid form that gets accumulated in various organs, including the heart. To contrive effective therapeutics against this debilitating congenital disorder, it is imperative to comprehend the structural ramifications induced by mutations in APoA1's dynamic conformation. Till now, several point mutations have been implicated in ApoA1's amyloidosis, although only a handful has been examined considerably. Especially, the single nucleotide polymorphisms (SNPs) that occur in-between 170-178 mutation hotspot site of APoA1 needs to be investigated, since most of them are culpable of amyloid deposition in the heart. To that effect, in the present study, we have computationally quantified and studied the ApoA1's biomolecular modifications fostered by SNPs in the 170-178 mutation hotspot. Findings from discrete molecular dynamics simulation studies indicate that the SNPs have noticeably steered the ApoA1's behaviour from its native structural dynamics. Analysis of protein's secondary structural changes exhibits a considerable change upon mutations. Further, subjecting the protein structures to simulated thermal denaturation shows increased resistance to denaturation among mutants when compared to native. Further, normal mode analysis of protein's dynamic motion also shows discrepancy in its dynamic structural change upon SNP. These structural digressions induced by SNPs can very well be the biomolecular incendiary that drives ApoA1 into its amyloidogenesis. And, understanding these structural modifications initiates a better understanding of SNP's amyloidogenic pathology on APoA1.Communicated by Ramaswamy H. Sarma.
MeSH term(s)	Humans ; Point Mutation ; Mutation ; Molecular Dynamics Simulation ; Amyloidosis ; Amyloid/genetics ; Apolipoprotein A-I/genetics
Chemical Substances	Amyloid ; APOA1 protein, human ; Apolipoprotein A-I
Language	English
Publishing date	2021-10-06
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	10.1080/07391102.2021.1986134
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Article ; Online: Unravelling the molecular effect of ocellatin-1, F1, K1 and S1, the frog-skin antimicrobial peptides to enhance its therapeutics-quantum and molecular mechanical approaches.

Sekar, P Chandra / Paul, D Meshach / Srinivasan, E / Rajasekaran, R

Journal of molecular modeling

2021 Volume 27, Issue 1, Page(s) 10

Abstract: Ocellatin AMPs (antimicrobial peptides) are considered to be promising alternative therapeutics to conventional antibiotics. Three-dimensional (3D) structures of ocellatin-F1 with 25 residues have been reported to be potent in terms of bacterial membrane ...

Abstract	Ocellatin AMPs (antimicrobial peptides) are considered to be promising alternative therapeutics to conventional antibiotics. Three-dimensional (3D) structures of ocellatin-F1 with 25 residues have been reported to be potent in terms of bacterial membrane permeability. To investigate the influence of similar ocellatin peptides with 25 residues pertaining to antimicrobial effect, ocellatin-1, K1 and S1 peptides were modelled with ocellatin-F1 as template. Comparative analyses between these peptides were carried out, using computational approaches. From the results of in silico toxicity profile, all peptides were found to be non-toxic with no haemolytic activity. Further sequence analysis, net charge, hydrophobicity and hydrophobic moment revealed the membrane permeable efficacy of ocellatin-1 peptide. Besides, the investigation of peptide electronic structures through density functional theory and quantum chemical (HOMO and LUMO) calculations predicted ocellatin-1 to be a suitable peptide, which can be used as a scaffold for therapeutics. Furthermore, the determination of structural contours such as RMSD, RMSF and Rg through trajectory analysis revealed that ocellatin-1 exhibited strong structural stability. In addition, the trajectory analysis of elements of secondary structure illustrated the alpha helical conformations to be retained in all peptides, except ocellatin-1. On the aforementioned grounds, ocellatin-1 was found to possess the important role of peptide penetration of the bacterial membrane. This study becomes significant, since it is the first time where the structural importance of ocellatin peptides were explored in detail and the therapeutic potential of ocellatin-1 as a peptide-based antimicrobial drug have been theoretically revealed.
MeSH term(s)	Amino Acid Sequence ; Animals ; Antimicrobial Cationic Peptides/chemistry ; Antimicrobial Cationic Peptides/metabolism ; Antimicrobial Cationic Peptides/pharmacology ; Anura/metabolism ; Computational Biology ; Computer Simulation ; Protein Structure, Secondary ; Sequence Analysis, Protein ; Skin/chemistry
Chemical Substances	Antimicrobial Cationic Peptides ; ocellatin 1 protein, Leptodactylus ocellatus
Language	English
Publishing date	2021-01-03
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/s00894-020-04652-6
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Article ; Online: Dayara bugyal restoration model in the alpine and subalpine region of the Central Himalaya: a step toward minimizing the impacts.

Kuniyal, Jagdish Chandra / Maiti, Priyanka / Kumar, Sandeep / Kumar, Anand / Bisht, Nisha / Sekar, K Chandra / Arya, Satish Chandra / Rai, Sumit / Nand, Mahesha

Scientific reports

2021 Volume 11, Issue 1, Page(s) 16547

Abstract: ... ground vegetation profile and below ground soil nutrient profile (N, P, K, pH and water holding capacity) were ...

Abstract	Eco-restoration initiative work in the high altitude Dayara pastureland (3501 m) from the Indian Himalayan Region has been considered to be one of the successful field demonstration against both natural and anthropogenic degradation. The present study therefore attempts to assess the implications of entire eco-restoration model as practiced by Department of Forest, Government of Uttarakhand in 2019. Its assessment was done by calculating restoration success index by way of considering three categories, viz., direct management measure (M), environmental desirability (E) and socio-economic feasibility (SE) considering 22 individual variables. 'M' comprised both biotic and abiotic pressures. Grazing and tourism were biotic, while abiotic pressure was considered mainly soil erosion in alpine area due to topographic fragility. Above ground vegetation profile and below ground soil nutrient profile (N, P, K, pH and water holding capacity) were analyzed in 'E' component. In the last but not least, 'SE' was analyzed to assess the social acceptability of the local communities and stakeholders who are supposed to be ultimate beneficiary of alike interventions. Direct management measure was found with the variable index score of 0.8 indicating the higher score as compared to environmental desirability (0.56). Under direct management measure, grazing and tourists' carrying capacity of the area was analyzed with high management needs to call the region sustainable in terms of availability of bio-resources. The ecosystem index score was evaluated for the reference (81.94), treated (64.5) and untreated zones (52.03), wherein increasing profile of these values were found. The outcomes like improved vegetation profile in terms of total herb density, soil nutrient profile of the restored area along with soil pH (4.96) and water holding capacity (49.85%) were found to be restored significantly along with controlling 169.64 tonne year
Language	English
Publishing date	2021-08-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-95472-y
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Article ; Online: Molecular simulation probes the potency of resveratrol in regulating the toxic aggregation of mutant V30M TTR fibrils in Transthyretin mediated amyloidosis.

Chandrasekhar, G / Srinivasan, E / Sekar, P Chandra / Venkataramanan, S / Rajasekaran, R

Journal of molecular graphics & modelling

2021 Volume 110, Page(s) 108055

Abstract: Transthyretin (TTR) mediated amyloidosis is a highly ruinous illness that affects various organs by aggravating the deposition of misfolded or mutated TTR protein aggregates in tissues. Hence, hindering the formation of TTR amyloid aggregates could be a ... ...

Abstract	Transthyretin (TTR) mediated amyloidosis is a highly ruinous illness that affects various organs by aggravating the deposition of misfolded or mutated TTR protein aggregates in tissues. Hence, hindering the formation of TTR amyloid aggregates could be a key strategy in finding an effective cure towards the aggravating disorder. In this analysis, we examined the subversive nature of point mutation, V30M, in TTR that promotes amyloidogenicity using discrete molecular dynamics (DMD) simulations. Besides, we probed the association of naturally occurring polyphenols: EGCG (a proven anti TTR aggregation agent as positive control), resveratrol and curcumin in mitigating the pathogenic repercussions of mutant TTR. Results from the computational studies endorsed that the resveratrol constitutes a restorative potential to subjugate TTR mediated amyloidosis, besides EGCG. Hence, this study could be a reminiscent aspect in understanding the inhibitory role of key polyphenols against the mutant TTR aggregates, which could be an aid towards structure-based drug design in the upcoming research era on familial amyloid disorders.
MeSH term(s)	Amyloid ; Amyloidosis/drug therapy ; Amyloidosis/genetics ; Humans ; Point Mutation ; Prealbumin/genetics ; Resveratrol
Chemical Substances	Amyloid ; Prealbumin ; Resveratrol (Q369O8926L)
Language	English
Publishing date	2021-10-15
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1396450-1
ISSN	1873-4243 ; 1093-3263
ISSN (online)	1873-4243
ISSN	1093-3263
DOI	10.1016/j.jmgm.2021.108055
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Article ; Online: NBN Gene Analysis and it's Impact on Breast Cancer.

Nithya, P / ChandraSekar, A

Journal of medical systems

2019 Volume 43, Issue 8, Page(s) 270

Abstract: Single Nucleotide Polymorphism (SNP) researches have become essential in finding out the congenital relationship of structural deviations with quantitative traits, heritable diseases and physical responsiveness to different medicines. NBN is a protein ... ...

Abstract	Single Nucleotide Polymorphism (SNP) researches have become essential in finding out the congenital relationship of structural deviations with quantitative traits, heritable diseases and physical responsiveness to different medicines. NBN is a protein coding gene (Breast Cancer); Nibrin is used to fix and rebuild the body from damages caused because of strand breaks (both singular and double) associated with protein nibrin. NBN gene was retrieved from dbSNP/NCBI database and investigated using computational SNP analysis tools. The encrypted region in SNPs (exonal SNPs) were analyzed using software tools, SIFT, Provean, Polyphen, INPS, SNAP and Phd-SNP. The 3'ends of SNPs in un-translated region were also investigated to determine the impact of binding. The association of NBN gene polymorphism leads to several diseases was studied. Four SNPs were predicted to be highly damaged in coding regions which are responsible for the diseases such as, Aplastic Anemia, Nijmegan breakage syndrome, Microsephaly normal intelligence, immune deficiency and hereditary cancer predisposing syndrome (clivar). The present study will be helpful in finding the suitable drugs in future for various diseases especially for breast cancer.
MeSH term(s)	Breast Neoplasms/genetics ; Cell Cycle Proteins/genetics ; Databases, Genetic ; Humans ; Nuclear Proteins/genetics ; Polymorphism, Single Nucleotide
Chemical Substances	Cell Cycle Proteins ; NBN protein, human ; Nuclear Proteins
Language	English
Publishing date	2019-07-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	423488-1
ISSN	1573-689X ; 0148-5598
ISSN (online)	1573-689X
ISSN	0148-5598
DOI	10.1007/s10916-019-1328-z
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Article: Prediction of Covid-19 symptoms with chest x-ray to optimize the solution through the MCOA Algorithm for feature extraction and measurement.

Natrajan, Prabhakaran / Prasad Sekar, Anandha / Murugan, Kamali / Sabarinathan, Chandrasekar / Chandra, Inbaraj / Prabhu, Venkatesan

Pakistan journal of pharmaceutical sciences

2023 Volume 36, Issue 1, Page(s) 111–119

Abstract: Due to poor understanding and inconsistent knowledge about covid-19 symptoms, the survival rate will decrease anywhere in the world. Every person who lives in the world should aware of COVID-19 symptoms to protect their life and hence increase the ... ...

Abstract	Due to poor understanding and inconsistent knowledge about covid-19 symptoms, the survival rate will decrease anywhere in the world. Every person who lives in the world should aware of COVID-19 symptoms to protect their life and hence increase the mortality rate of humans. The Indian government took precautions to lower the fatality rate, which includes hand sanitizer, wearing NS2 masks and keeping social distance to live a long life. The proposed method uses the MCOA-modified cat optimization algorithm to extract the image features and predict them in earlier stages and diagnosis. Furthermore, the proposed method clusters the chest image concerning size, shape and intensity concerning the irregular edges present in the chest imaging. The proposed MCAO algorithm cluster the chest image with an accuracy of about 95% and fit into the solution space with the state of art. The problem of the concave region present in the image is clustered in the solution space to delineate the parameters of pneumonia, fever, mucus fluid and respiration rate. The method gives the solution to the radiologist to detect earlier covid 19 symptoms for feature extraction and measurement.
MeSH term(s)	Humans ; Algorithms ; Awareness ; COVID-19/diagnostic imaging ; X-Rays
Language	English
Publishing date	2023-03-27
Publishing country	Pakistan
Document type	Journal Article
ZDB-ID	885131-1
ISSN	1011-601X
ISSN	1011-601X
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Article ; Online: Novel approaches on identification of conserved miRNAs for broad-spectrum Potyvirus control measures.

Sankaranarayanan, Ramamoorthy / Palani, Sankara Naynar / Tamilmaran, Nagarajan / Punitha Selvakumar, A S / Chandra Sekar, P / Tennyson, Jebasingh

Molecular biology reports

2021 Volume 48, Issue 3, Page(s) 2377–2388

Abstract: Potyviridae comprises more than 200 ssRNA viruses, many of which have a broad host range and geographical distributions. Potyvirids (members of Potyviridae) infect several economically important plants such as saffron, cardamom, cucumber, pepper, potato, ...

Abstract	Potyviridae comprises more than 200 ssRNA viruses, many of which have a broad host range and geographical distributions. Potyvirids (members of Potyviridae) infect several economically important plants such as saffron, cardamom, cucumber, pepper, potato, tomato, yam, etc. Cumulatively, potyvirids cause a substantial economic loss. The major bottleneck in developing an efficient antiviral strategy is that viruses quickly evade host immunity owing to their higher mutation and recombination rates. Due to this reason, the emergence of newer and improved broad-spectrum approaches to combat viral infections is essential. The use of microRNA's (miRNA) to circumvent viral infection against animal viruses has been successfully employed. Fewer studies reported the development of efficient miRNA-based antivirus resistant strategies against plant viruses and none focused on multiple virus resistance. We focused on potyviruses since studies are limited and identification of conserved miRNAs among various host plants would be an initiative to design broad-spectrum antivirus strategies. In this study, we predicted evolutionarily conserved miRNAs by BLAST searching of reported miRNAs from 15 plants against the GSS and EST sequences of banana. A total of nine miRNAs were predicted and screened in nine diverse potyvirids' hosts (Banana, Tomato, Green gram, Jasmine, Chilli, Coriander, Onion, Rose and Colocasia) belonging to eight different orders (Zingiberales, Solanales, Fabales, Lamiales, Apiales, Asperagales, Rosales and Alismatales). Results suggested that miR168 and miR162 are conserved among all the selected plants. This comprehensive study laid the foundations to design broad-spectrum antivirus resistance using miRNAs. To conclude miR168 and miR162 are conserved among many plants and play a crucial role in evading virus infection which could be used as a potential candidate for developing antiviral strategies against potyvirid infections.
MeSH term(s)	Conserved Sequence/genetics ; Gene Expression Regulation, Plant ; MicroRNAs/chemistry ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Molecular Sequence Annotation ; Nucleic Acid Conformation ; Plant Diseases/genetics ; Plant Diseases/prevention & control ; Plant Diseases/virology ; Plants/genetics ; Plants/virology ; Potyvirus/physiology
Chemical Substances	MicroRNAs
Language	English
Publishing date	2021-03-20
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	186544-4
ISSN	1573-4978 ; 0301-4851
ISSN (online)	1573-4978
ISSN	0301-4851
DOI	10.1007/s11033-021-06271-7
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Article: Characterization Studies of Natural Cellulosic Fibers Extracted from Shwetark Stem

Raja, K. / Prabu, B. / Ganeshan, P. / Sekar, V. S. Chandra / NagarajaGanesh, B.

Journal of natural fibers

2021 Volume 18, Issue 10/12, Page(s) 1934

Language	English
Document type	Article
ZDB-ID	2182715-1
ISSN	1544-0478
Database	Current Contents Nutrition, Environment, Agriculture

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