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  1. Article ; Online: Molecular insights into the potential effects of selective estrogen receptor β agonists in Alzheimer's and Parkinson's diseases.

    Rymbai, Emdormi / Sugumar, Deepa / Chakkittukandiyil, Amritha / Kothandan, Ram / Selvaraj, Divakar

    Cell biochemistry and function

    2024  Volume 42, Issue 3, Page(s) e4014

    Abstract: Alzheimer's disease (AD) and Parkinson's disease (PD) are the most common neurodegenerative disorders. Pathologically, AD and PD are characterized by the accumulation of misfolded proteins. Hence, they are also called as proteinopathy diseases. Gender is ...

    Abstract Alzheimer's disease (AD) and Parkinson's disease (PD) are the most common neurodegenerative disorders. Pathologically, AD and PD are characterized by the accumulation of misfolded proteins. Hence, they are also called as proteinopathy diseases. Gender is considered as one of the risk factors in both diseases. Estrogens are widely accepted to be neuroprotective in several neurodegenerative disorders. Estrogens can be produced in the central nervous system, where they are called as neurosteroids. Estrogens mediate their neuroprotective action mainly through their actions on estrogen receptor alpha (ERα) and estrogen receptor beta (ERβ). However, ERα is mainly involved in the growth and development of the primary and secondary sexual organs in females. Hence, the activation of ERα is associated with undesired side effects such as gynecomastia and increase in the risk of breast cancer, thromboembolism, and feminization. Therefore, selective activation of ERβ is often considered to be safer. In this review, we explore the role of ERβ in regulating the expression and functions of AD- and PD-associated genes. Additionally, we discuss the association of these genes with the amyloid-beta peptide (Aβ) and α-synuclein mediated toxicity. Ultimately, we established a correlation between the importance of ERβ activation and the process underlying ERβ's neuroprotective mechanisms in AD and PD.
    MeSH term(s) Female ; Male ; Humans ; Parkinson Disease/drug therapy ; Estrogens/pharmacology ; Estrogen Receptor beta/genetics ; Estrogen Receptor alpha/genetics ; Alzheimer Disease/drug therapy
    Chemical Substances Estrogens ; Estrogen Receptor beta ; Estrogen Receptor alpha
    Language English
    Publishing date 2024-04-14
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 283643-9
    ISSN 1099-0844 ; 0263-6484
    ISSN (online) 1099-0844
    ISSN 0263-6484
    DOI 10.1002/cbf.4014
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Handling class imbalance problem in miRNA dataset associated with cancer.

    Kothandan, Ram

    Bioinformation

    2015  Volume 11, Issue 1, Page(s) 6–10

    Abstract: MiRNAs are small (~22nt long) non-coding RNA sequences; binds to the complementarity target sites in 3' Untranslated Region (UTR) of mRNA sequences but not restricted to other mRNA regions viz., 5' UTR and Coding sequences (CDS). Complementarity binding ... ...

    Abstract MiRNAs are small (~22nt long) non-coding RNA sequences; binds to the complementarity target sites in 3' Untranslated Region (UTR) of mRNA sequences but not restricted to other mRNA regions viz., 5' UTR and Coding sequences (CDS). Complementarity binding of miRNA to mRNA target sites either results in complete degradation of the mRNA itself or it may regulate the mRNA as an oncogene or as a tumor suppressor gene. However, the exact mechanism involved in identifying a miRNA to be associated with cancer is still unclear. Further, with the outburst in the number of miRNAs sequences recorded every year in miRBase, the gap is still widening mainly due to the laborious and economically unfavorable experimental procedures associated with the functional annotation. Motivated by the fact, we constructed a two-step support vector machine-based predictive model - miRSEQ and miRINT. However, the major pitfall during the construction of the model is the class imbalance problem. Hence, in order to overcome class imbalance problem, in the present study we empirically compare the effectiveness of two different methods viz., Synthetic Minority Oversampling Technique (SMOTE) and cost-senstive learning method. Performance measures were evaluated in terms of Precision and Recall. Based on our result, it was observed that for miRNA dataset with high class imbalance utilized for predicting association of cancer, cost-sensitive method outperformed the oversampling method.
    Language English
    Publishing date 2015-01-30
    Publishing country Singapore
    Document type Journal Article
    ZDB-ID 2203786-X
    ISSN 0973-2063
    ISSN 0973-2063
    DOI 10.6026/97320630011006
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: A quinoline alkaloid potentially modulates the amyloidogenic structural transitions of the biofilm scaffolding small basic protein.

    Admane, Nikita / Kothandan, Ram / Syed, Sowfia / Biswas, Sumit

    Journal of biomolecular structure & dynamics

    2021  Volume 41, Issue 4, Page(s) 1366–1377

    Abstract: Bacterial biofilm formation by communities of opportunistic bacterial pathogens ... ...

    Abstract Bacterial biofilm formation by communities of opportunistic bacterial pathogens like
    MeSH term(s) Biofilms ; Amyloid/metabolism ; Alkaloids/pharmacology ; Camptothecin/pharmacology ; Quinolines/pharmacology
    Chemical Substances Amyloid ; Alkaloids ; Camptothecin (XT3Z54Z28A) ; Quinolines
    Language English
    Publishing date 2021-12-29
    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 10.1080/07391102.2021.2020165
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Network-based drug repositioning of linagliptin as a potential agent for uterine fibroids targeting transforming growth factor-beta mediated fibrosis.

    Bhat, Anusha Shreenidhi / Chakkittukandiyil, Amritha / Muthu, Santhosh Kumar / Kotha, Satvik / Muruganandham, Sudharsan / Rajagopal, Kalirajan / Jayaram, Saravanan / Kothandan, Ram / Selvaraj, Divakar

    Biochemical and biophysical research communications

    2024  Volume 703, Page(s) 149611

    Abstract: Uterine fibroid is the most common non-cancerous tumor with no satisfactory options for long-term pharmacological treatment. Fibroblast activation protein-α (FAP) is one of the critical enzymes that enhances the fibrosis in uterine fibroids. Through ... ...

    Abstract Uterine fibroid is the most common non-cancerous tumor with no satisfactory options for long-term pharmacological treatment. Fibroblast activation protein-α (FAP) is one of the critical enzymes that enhances the fibrosis in uterine fibroids. Through STITCH database mining, we found that dipeptidyl peptidase-4 inhibitors (DPP4i) have the potential to inhibit the activity of FAP. Both DPP4 and FAP belong to the dipeptidyl peptidase family and share a similar catalytic domain. Hence, ligands which have a binding affinity with DPP4 could also bind with FAP. Among the DPP4i, linagliptin exhibited the highest binding affinity (Dock score = -8.562 kcal/mol) with FAP. Our study uncovered that the differences in the S
    MeSH term(s) Rats ; Animals ; Female ; Linagliptin/pharmacology ; Linagliptin/therapeutic use ; Transforming Growth Factor beta ; Dipeptidyl Peptidase 4/metabolism ; Drug Repositioning ; Dipeptidyl-Peptidase IV Inhibitors/pharmacology ; Dipeptidyl-Peptidase IV Inhibitors/therapeutic use ; Fibrosis ; Leiomyoma/drug therapy ; Collagen ; Transforming Growth Factors
    Chemical Substances Linagliptin (3X29ZEJ4R2) ; Transforming Growth Factor beta ; Dipeptidyl Peptidase 4 (EC 3.4.14.5) ; Dipeptidyl-Peptidase IV Inhibitors ; Collagen (9007-34-5) ; Transforming Growth Factors (76057-06-2)
    Language English
    Publishing date 2024-02-08
    Publishing country United States
    Document type Journal Article
    ZDB-ID 205723-2
    ISSN 1090-2104 ; 0006-291X ; 0006-291X
    ISSN (online) 1090-2104 ; 0006-291X
    ISSN 0006-291X
    DOI 10.1016/j.bbrc.2024.149611
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: The identification of cianidanol as a selective estrogen receptor beta agonist and evaluation of its neuroprotective effects on Parkinson's disease models.

    Rymbai, Emdormi / Sugumar, Deepa / Chakkittukandiyil, Amritha / Kothandan, Ram / Selvaraj, Jubie / Selvaraj, Divakar

    Life sciences

    2023  Volume 333, Page(s) 122144

    Abstract: Aim: The present study aims to identify selective estrogen receptor beta (ERβ) agonists and to evaluate the neuroprotective mechanism in Parkinson's disease (PD) models.: Main methods: In-silico studies were carried out using Maestro and GROMACS. ... ...

    Abstract Aim: The present study aims to identify selective estrogen receptor beta (ERβ) agonists and to evaluate the neuroprotective mechanism in Parkinson's disease (PD) models.
    Main methods: In-silico studies were carried out using Maestro and GROMACS. Neuroprotective activity and apoptosis were evaluated using cytotoxicity assay and flow cytometry respectively. Gene expression studies were carried out by reverse transcription polymerase chain reaction. Motor and cognitive functions were assessed by actophotometer, rotarod, catalepsy, and elevated plus maze. The neuronal population in the substantia nigra and striatum of rats was assessed by hematoxylin and eosin staining.
    Key findings: Cianidanol was identified as a selective ERβ agonist through virtual screening. The cianidanol-ERβ complex is stable during the 200 ns simulation and was able to retain the interactions with key amino acid residues. Cianidanol (25 μM) prevents neuronal toxicity and apoptosis induced by rotenone in differentiated SH-SY5Y cells. Additionally, cianidanol (25 μM) increases the expression of ERβ, cathepsin D, and Nrf2 transcripts. The neuroprotective effects of cianidanol (25 μM) were reversed in the presence of a selective ERβ antagonist. In this study, we found that selective activation of ERβ could decrease the transcription of α-synuclein gene. Additionally, cianidanol (10, 20, 30 mg/kg, oral) improves the motor and cognitive deficit in rats induced by rotenone.
    Significance: Cianidanol shows neuroprotective action in PD models and has the potential to serve as a novel therapeutic agent for the treatment of PD.
    MeSH term(s) Rats ; Humans ; Animals ; Parkinson Disease/drug therapy ; Parkinson Disease/metabolism ; Neuroprotective Agents/pharmacology ; Neuroprotective Agents/therapeutic use ; Estrogen Receptor beta ; Catechin/therapeutic use ; Rotenone/pharmacology ; Neuroblastoma/drug therapy ; Estrogens/therapeutic use ; Disease Models, Animal
    Chemical Substances Neuroprotective Agents ; Estrogen Receptor beta ; Catechin (8R1V1STN48) ; Rotenone (03L9OT429T) ; Estrogens
    Language English
    Publishing date 2023-10-04
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 3378-9
    ISSN 1879-0631 ; 0024-3205
    ISSN (online) 1879-0631
    ISSN 0024-3205
    DOI 10.1016/j.lfs.2023.122144
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Search for RNA aptamers against non-structural protein of SARS-CoV-2: Design using molecular dynamics approach.

    Kothandan, Ram / Uthayasooriyan, Pavithra / Vairamani, Sivaranjani

    Beni-Suef University journal of basic and applied sciences

    2021  Volume 10, Issue 1, Page(s) 64

    Abstract: Background: Recent outbreak of deadly Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) urges the scientist to identify the potential vaccine or drug to control the disease. SARS-CoV-2 with its single stranded RNA genome (length ~ 30 kb) is ... ...

    Abstract Background: Recent outbreak of deadly Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) urges the scientist to identify the potential vaccine or drug to control the disease. SARS-CoV-2 with its single stranded RNA genome (length ~ 30 kb) is enveloped with active spike proteins. The genome is non-segmental with 5'-cap and 3'-poly tail and acts as a mRNA for the synthesis of replicase polyproteins. The replicase gene lying downstream to 5'-end encodes for non-structural protein, which in turn pose multiple functions ranging from envelope to nucleocapsid development. This study aims to identify the highly stable, effective and less toxic single strand RNA-based aptamers against non-structural protein 10 (NSP10). NSP10 is the significant activator of methyltransferase enzymes (NSP14 and NSP16) in SARS-CoV-2. Inhibiting the activation of methyltransferase leads to partial viral RNA capping or lack of capping, which makes the virus particles susceptible to host defence system.
    Results: In this study, we focused on designing RNA aptamers through computational approach, docking of protein-aptamer followed by molecular dynamics simulation to perceive the binding stability of complex. Docking study reveals the high binding affinity of three aptamers namely RNA-053, 001, 010 to NSP10 with the HADDOCK score of - 88.5 ± 7.0, - 87.7 ± 11.5, - 86.1 ± 12 respectively. Molecular Dynamics suggests high conformational stability between the aptamer and the protein. Among the screened aptamers two aptamers maintained at least 3-4 intermolecular H-bonds throughout the simulation period.
    Conclusions: The study identifies the potential aptamer candidate against less investigated but significant antiviral target i.e., NSP10/NSP16 interface complex.
    Supplementary information: The online version contains supplementary material available at 10.1186/s43088-021-00152-5.
    Language English
    Publishing date 2021-10-12
    Publishing country England
    Document type Journal Article
    ZDB-ID 2768279-1
    ISSN 2314-8543 ; 2314-8535 ; 2314-8543
    ISSN (online) 2314-8543
    ISSN 2314-8535 ; 2314-8543
    DOI 10.1186/s43088-021-00152-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Improved laccase production from

    Chenthamara, Dhrisya / Sivaramakrishnan, Muthusaravanan / Ramakrishnan, Sankar Ganesh / Esakkimuthu, Sivakumar / Kothandan, Ram / Subramaniam, Sadhasivam

    3 Biotech

    2022  Volume 12, Issue 12, Page(s) 346

    Abstract: Fungal laccases are versatile biocatalyst and occupy a prominent place in various industrial applications due to its broad substrate specificity. The simplest method to enhance the laccase production is by usage of cheap substrates in the fermentation ... ...

    Abstract Fungal laccases are versatile biocatalyst and occupy a prominent place in various industrial applications due to its broad substrate specificity. The simplest method to enhance the laccase production is by usage of cheap substrates in the fermentation processes incorporating modeling approaches for optimization. Integrated biorefinery concept is receiving wide popularity by making use of various products from microalgal biomass. The research aimed to identify the potential of deoiled microalgal biomass (DMB), a waste product from algal biorefinery as a nutrient supplement to enhance laccase production in
    Supplementary information: The online version contains supplementary material available at 10.1007/s13205-022-03404-y.
    Language English
    Publishing date 2022-11-10
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2600522-0
    ISSN 2190-5738 ; 2190-572X
    ISSN (online) 2190-5738
    ISSN 2190-572X
    DOI 10.1007/s13205-022-03404-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Search for RNA aptamers against non-structural protein of SARS-CoV-2

    Ram Kothandan / Pavithra Uthayasooriyan / Sivaranjani Vairamani

    Beni-Suef University Journal of Basic and Applied Sciences, Vol 10, Iss 1, Pp 1-

    Design using molecular dynamics approach

    2021  Volume 12

    Abstract: Abstract Background Recent outbreak of deadly Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) urges the scientist to identify the potential vaccine or drug to control the disease. SARS-CoV-2 with its single stranded RNA genome (length ~ 30 ... ...

    Abstract Abstract Background Recent outbreak of deadly Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) urges the scientist to identify the potential vaccine or drug to control the disease. SARS-CoV-2 with its single stranded RNA genome (length ~ 30 kb) is enveloped with active spike proteins. The genome is non-segmental with 5’-cap and 3’-poly tail and acts as a mRNA for the synthesis of replicase polyproteins. The replicase gene lying downstream to 5’-end encodes for non-structural protein, which in turn pose multiple functions ranging from envelope to nucleocapsid development. This study aims to identify the highly stable, effective and less toxic single strand RNA-based aptamers against non-structural protein 10 (NSP10). NSP10 is the significant activator of methyltransferase enzymes (NSP14 and NSP16) in SARS-CoV-2. Inhibiting the activation of methyltransferase leads to partial viral RNA capping or lack of capping, which makes the virus particles susceptible to host defence system. Results In this study, we focused on designing RNA aptamers through computational approach, docking of protein-aptamer followed by molecular dynamics simulation to perceive the binding stability of complex. Docking study reveals the high binding affinity of three aptamers namely RNA-053, 001, 010 to NSP10 with the HADDOCK score of − 88.5 ± 7.0, − 87.7 ± 11.5, − 86.1 ± 12 respectively. Molecular Dynamics suggests high conformational stability between the aptamer and the protein. Among the screened aptamers two aptamers maintained at least 3-4 intermolecular H-bonds throughout the simulation period. Conclusions The study identifies the potential aptamer candidate against less investigated but significant antiviral target i.e., NSP10/NSP16 interface complex.
    Keywords SARS-CoV-2 ; Aptamer ; NSP10 ; Docking ; Molecular dynamics ; Medicine (General) ; R5-920 ; Science ; Q
    Subject code 572
    Language English
    Publishing date 2021-10-01T00:00:00Z
    Publisher SpringerOpen
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Virtual screening of phytochemical compounds as potential inhibitors against SARS-CoV-2 infection.

    Kothandan, Ram / Rajan, Cashlin Anna Suveetha Gnana / Arjun, Janamitra / Raj, Rejoe Raymond Michael / Syed, Sowfia

    Beni-Suef University journal of basic and applied sciences

    2021  Volume 10, Issue 1, Page(s) 9

    Abstract: Background: The present pandemic situation due to coronavirus has led to the search for newer prevention, diagnostic, and treatment methods. The onset of the corona infection in a human results in acute respiratory illness followed by death if not ... ...

    Abstract Background: The present pandemic situation due to coronavirus has led to the search for newer prevention, diagnostic, and treatment methods. The onset of the corona infection in a human results in acute respiratory illness followed by death if not diagnosed and treated with suitable antiretroviral drugs. With the unavailability of the targeted drug treatment, several repurposed drugs are being used for treatment. However, the side-effects of the drugs urges us to move to a search for newer synthetic- or phytochemical-based drugs. The present study investigates the use of various phytochemicals virtually screened from various plant sources in Western Ghats, India, and subsequently molecular docking studies were performed to identify the efficacy of the drug in retroviral infection particularly coronavirus infection.
    Results: Out of 57 phytochemicals screened initially based on the structural and physicochemical properties, 39 were effectively used for the docking analysis. Finally, 5 lead compounds with highest hydrophobic interaction and number of H-bonds were screened. Results from the interaction analysis suggest Piperolactam A to be pocketed well with good hydrophobic interaction with the residues in the binding region R1. ADME and toxicity profiling also reveals Piperolactam A with higher LogS values indicating higher permeation and hydrophilicity. Toxicity profiling suggests that the 5 screened compounds to be relatively safe.
    Conclusion: The in silico methods used in this study suggests that the compound Piperolactam A to be the most effective inhibitor of S-protein from binding to the GRP78 receptor. By blocking the binding of the S-protein to the CS-GRP78 cell surface receptor, they can inhibit the binding of the virus to the host.
    Supplementary information: The online version contains supplementary material available at 10.1186/s43088-021-00095-x.
    Language English
    Publishing date 2021-01-28
    Publishing country England
    Document type Journal Article
    ZDB-ID 2768279-1
    ISSN 2314-8543 ; 2314-8535 ; 2314-8543
    ISSN (online) 2314-8543
    ISSN 2314-8535 ; 2314-8543
    DOI 10.1186/s43088-021-00095-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Enterococcus faecalis thrives in dual-species biofilm models under iron-rich conditions.

    Govindarajan, Deenadayalan Karaiyagowder / Meghanathan, Yogesan / Sivaramakrishnan, Muthusaravanan / Kothandan, Ram / Muthusamy, Ananthasubramanian / Seviour, Thomas William / Kandaswamy, Kumaravel

    Archives of microbiology

    2022  Volume 204, Issue 12, Page(s) 710

    Abstract: Escherichia coli (E. coli) and Enterococcus faecalis (E. faecalis) are pathogenic strains that often coexist in intestinal flora of humans and are prone to cause biofilm-associated infections, such as gastrointestinal tract and urinary tract infections. ... ...

    Abstract Escherichia coli (E. coli) and Enterococcus faecalis (E. faecalis) are pathogenic strains that often coexist in intestinal flora of humans and are prone to cause biofilm-associated infections, such as gastrointestinal tract and urinary tract infections. Earlier studies have demonstrated that E. faecalis biofilm can metabolize ferrous ions in iron-rich environments and promote biofilm growth under in-vivo conditions. However, the influence of iron transporters on dual-species biofilm growth and the nature of molecular-level interactions between iron transporter proteins and Fe
    MeSH term(s) Humans ; Enterococcus faecalis ; Escherichia coli/metabolism ; Biofilms ; Urinary Tract Infections/microbiology ; Iron/metabolism ; Carrier Proteins/metabolism
    Chemical Substances Iron (E1UOL152H7) ; Carrier Proteins
    Language English
    Publishing date 2022-11-16
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 124824-8
    ISSN 1432-072X ; 0302-8933
    ISSN (online) 1432-072X
    ISSN 0302-8933
    DOI 10.1007/s00203-022-03309-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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