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  1. Article ; Online: Crystal structure, intermolecular interactions, charge-density distribution and ADME properties of the acridinium 4-nitrobenzoate and 2-amino-3-methylpyridinium 4-nitrobenzoate salts: a combined experimental and theoretical study.

    Balasubramanian, Hemalatha / Mariappan, Petchi Raman / Poomani, Kumaradhas

    Acta crystallographica. Section C, Structural chemistry

    2024  Volume 80, Issue Pt 4, Page(s) 115–122

    Abstract: Acridines are a class of bioactive agents which exhibit high biological stability and the ability to intercalate with DNA; they have a wide range of applications. Pyridine derivatives have a wide range of biological activities. To enhance the properties ... ...

    Abstract Acridines are a class of bioactive agents which exhibit high biological stability and the ability to intercalate with DNA; they have a wide range of applications. Pyridine derivatives have a wide range of biological activities. To enhance the properties of acridine and 2-amino-3-methylpyridine as the active pharmaceutical ingredient (API), 4-nitrobenzoic acid was chosen as a coformer. In the present study, a mixture of acridine and 4-nitrobenzoic acid forms the salt acridinium 4-nitrobenzoate, C
    MeSH term(s) Crystallography, X-Ray ; Salts/chemistry ; Hydrogen Bonding ; Nitrobenzoates/chemistry ; Models, Theoretical ; Acridines ; Aminopyridines ; Picolines
    Chemical Substances 2-amino-3-methylpyridine (Y2WWD85QY6) ; Salts ; 4-nitrobenzoic acid (G83NWR61OW) ; Nitrobenzoates ; Acridines ; Aminopyridines ; Picolines
    Language English
    Publishing date 2024-03-19
    Publishing country England
    Document type Journal Article
    ZDB-ID 2025703-X
    ISSN 2053-2296 ; 1600-5759 ; 0108-2701
    ISSN (online) 2053-2296 ; 1600-5759
    ISSN 0108-2701
    DOI 10.1107/S2053229624002250
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  2. Article ; Online: Lawsonia inermis

    Shahanaj, Ismail / Ramakrishnan, Jaganathan / Poomani, Kumaradhas / Devarajan, Natarajan

    Journal of biomolecular structure & dynamics

    2023  Volume 41, Issue 23, Page(s) 13752–13765

    Abstract: ... Lawsonia ... ...

    Abstract Lawsonia inermis
    MeSH term(s) Animals ; Humans ; alpha-Glucosidases/metabolism ; Plant Extracts/pharmacology ; Plant Extracts/chemistry ; Molecular Dynamics Simulation ; Lawsonia Plant/metabolism ; Diabetes Mellitus, Type 2 ; Molecular Docking Simulation ; Acetylcholinesterase/metabolism ; Flowers/chemistry ; Flowers/metabolism ; Phytochemicals/pharmacology ; Phytochemicals/chemistry ; Antioxidants/pharmacology ; Antioxidants/chemistry ; Mammals/metabolism
    Chemical Substances alpha-Glucosidases (EC 3.2.1.20) ; Plant Extracts ; Acetylcholinesterase (EC 3.1.1.7) ; di-N',N''-methylglyoxal bis(guanylhydrazone) (66002-86-6) ; Phytochemicals ; Antioxidants
    Language English
    Publishing date 2023-03-11
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2023.2179546
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    Zs.A 2093: Show issues Location:
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  3. Article ; Online: Binding properties of selective inhibitors of P323L mutated RdRp of SARS-CoV-2: a combined molecular screening, docking and dynamics simulation study.

    Chinnamadhu, Archana / Ramakrishnan, Jaganathan / Suresh, Suganya / Poomani, Kumaradhas

    Journal of biomolecular structure & dynamics

    2023  Volume 42, Issue 8, Page(s) 4283–4296

    Abstract: Since 2019 the SARS-CoV-2 and its variants caused COVID-19, such incidents brought the world in pandemic situation. This happened due to furious mutations in SARS-CoV-2, in which some variants had high transmissibility and infective, this led the virus ... ...

    Abstract Since 2019 the SARS-CoV-2 and its variants caused COVID-19, such incidents brought the world in pandemic situation. This happened due to furious mutations in SARS-CoV-2, in which some variants had high transmissibility and infective, this led the virus emerged as virulent and worsened the COVID-19 situation. Among the variants, P323L is one of the important mutants of RdRp in SARS-CoV-2. To inhibit the erroneous function of this mutated RdRp, we have screened 943 molecules against the P323L mutated RdRp with the criteria that the molecules with 90% similar to the structure of remdesivir (control drug) resulted nine molecules. Further, these molecules were evaluated by induced fit docking (IFD) identified two molecules (M2 & M4) which are forming strong intermolecular interactions with the key residues of mutated RdRp and has high binding affinity. Docking score of the M2 and M4 molecules with mutated RdRp are -9.24 and -11.87 kcal/mol, respectively. Further, to understand the intermolecular interactions, conformational stability, the molecular dynamics simulation and binding free energy calculations were performed. The binding free energy values of M2 and M4 molecules with the P323L mutated RdRp complexes are -81.60 and -83.07 kcal/mol, respectively. The results of this
    MeSH term(s) Humans ; Adenosine Monophosphate/analogs & derivatives ; Adenosine Monophosphate/pharmacology ; Adenosine Monophosphate/chemistry ; Adenosine Monophosphate/metabolism ; Alanine/analogs & derivatives ; Alanine/chemistry ; Antiviral Agents/pharmacology ; Antiviral Agents/chemistry ; Binding Sites ; Coronavirus RNA-Dependent RNA Polymerase/antagonists & inhibitors ; Coronavirus RNA-Dependent RNA Polymerase/chemistry ; Coronavirus RNA-Dependent RNA Polymerase/metabolism ; Coronavirus RNA-Dependent RNA Polymerase/genetics ; COVID-19/virology ; COVID-19 Drug Treatment ; Molecular Docking Simulation/methods ; Molecular Dynamics Simulation ; Mutation ; Protein Binding ; SARS-CoV-2/drug effects ; SARS-CoV-2/enzymology ; SARS-CoV-2/genetics
    Chemical Substances Adenosine Monophosphate (415SHH325A) ; Alanine (OF5P57N2ZX) ; Antiviral Agents ; Coronavirus RNA-Dependent RNA Polymerase (EC 2.7.7.48) ; remdesivir (3QKI37EEHE) ; NSP12 protein, SARS-CoV-2 (EC 2.7.7.48)
    Language English
    Publishing date 2023-06-10
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2023.2219762
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  4. Article ; Online: Probing the binding nature and stability of highly transmissible mutated variant alpha to omicron of SARS-CoV-2 RBD with ACE2 via molecular dynamics simulation.

    Ramakrishnan, Jaganathan / Chinnamadhu, Archana / Suresh, Suganya / Poomani, Kumaradhas

    Journal of cellular biochemistry

    2023  Volume 124, Issue 8, Page(s) 1115–1134

    Abstract: Currently, no approved drug is available as a causative agent of coronavirus disease 2019 (COVID-19) except for some repurposed drugs. The first structure of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was reported in late 2019, based on ...

    Abstract Currently, no approved drug is available as a causative agent of coronavirus disease 2019 (COVID-19) except for some repurposed drugs. The first structure of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was reported in late 2019, based on that some vaccines and repurposed drugs were approved to prevent people from COVID-19 during the pandemic situation. Since then, new types of variants emerged and notably, the receptor binding domain (RBD) adopted different binding modes with angiotensin-converting enzyme 2 (ACE2); this made significant changes in the progression of COVID-19. Some of the new variants are highly infectious spreading fast and dangerous. The present study is focused on understanding the binding mode of the RBD of different mutated SARS-CoV-2 variants of concern (alpha to omicron) with the human ACE2 using molecular dynamics simulation. Notably, some variants adopted a new binding mode of RBD with ACE2 and formed different interactions, which is unlike the wild type; this was confirmed from the comparison of interaction between RBD-ACE2 of all variants with its wild-type structure. Binding energy values confirm that some mutated variants exhibit high binding affinity. These findings demonstrate that the variations in the sequence of SARS-CoV-2 S-protein altered the binding mode of RBD; this may be the reason that the virus has high transmissibility and causes new infections. This in-silico study on mutated variants of SARS-CoV-2 RBD with ACE2 insights into their binding mode, binding affinity, and stability. This information may help to understand the RBD-ACE2 binding domains, which allows for designing newer drugs and vaccines.
    MeSH term(s) Humans ; Angiotensin-Converting Enzyme 2/genetics ; COVID-19 ; Molecular Dynamics Simulation ; Mutation ; Protein Binding ; SARS-CoV-2/genetics
    Chemical Substances Angiotensin-Converting Enzyme 2 (EC 3.4.17.23) ; spike protein, SARS-CoV-2
    Language English
    Publishing date 2023-07-12
    Publishing country United States
    Document type Journal Article
    ZDB-ID 392402-6
    ISSN 1097-4644 ; 0730-2312
    ISSN (online) 1097-4644
    ISSN 0730-2312
    DOI 10.1002/jcb.30432
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  5. Article ; Online: Investigation of intermolecular interactions and binding mechanism of PU139 and PU141 molecules with p300 HAT enzyme via molecular docking, molecular dynamics simulations and binding free energy analysis.

    Ramakrishnan, Jaganathan / Magudeeswaran, Sivanandam / Suresh, Suganya / Poomani, Kumaradhas

    Journal of biomolecular structure & dynamics

    2022  Volume 41, Issue 4, Page(s) 1351–1365

    Abstract: The p300 histone acetyltransferase (HAT) enzyme acetylates the lysine residue of histone promotes the transcription reaction. The abnormal function of p300 HAT enzyme causes various diseases such as Cancer, Asthma, Alzheimer, Diabetics, and AIDS. In the ... ...

    Abstract The p300 histone acetyltransferase (HAT) enzyme acetylates the lysine residue of histone promotes the transcription reaction. The abnormal function of p300 HAT enzyme causes various diseases such as Cancer, Asthma, Alzheimer, Diabetics, and AIDS. In the recent years, several studies have been conducted to design potential drug to inhibit this enzyme. Recently, an
    MeSH term(s) Molecular Dynamics Simulation ; Molecular Docking Simulation ; Histone Acetyltransferases/chemistry ; Catalytic Domain ; Histones/metabolism
    Chemical Substances Histone Acetyltransferases (EC 2.3.1.48) ; Histones
    Language English
    Publishing date 2022-01-03
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2021.2020164
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  6. Article ; Online: Phytochemical profiling, human insulin stability and alpha glucosidase inhibition of Gymnema latifolium leaves aqueous extract: Exploring through experimental and in silico approach.

    Ismail, Shahanaj / Chandel, Tajalli Ilm / Ramakrishnan, Jaganathan / Khan, Rizwan Hasan / Poomani, Kumaradhas / Devarajan, Natarajan

    Computational biology and chemistry

    2023  Volume 107, Page(s) 107964

    Abstract: Diabetes mellitus Type 2 (DM2T) is a rapidly expanding metabolic endocrine disorder worldwide. It is caused due to inadequate insulin secretion by pancreatic beta cells as well as development of insulin resistance. This study aimed to investigate the ... ...

    Abstract Diabetes mellitus Type 2 (DM2T) is a rapidly expanding metabolic endocrine disorder worldwide. It is caused due to inadequate insulin secretion by pancreatic beta cells as well as development of insulin resistance. This study aimed to investigate the anti-α-glucosidase, insulin stabilization effect, and non-cytotoxic nature of Gymnema latifolium leaf aqueous extract (GLAE). FTIR analysis revealed the functional groups of compounds present in GLAE. Through LC/ESI-MS/MS analysis, about 12 compounds which belongs to different classes, triterpene glycosides, flavonoids, phenolics, stilbene glycosides and chlorophenolic glycosides were identified. GLAE showed in vitro antioxidant activity. GLAE stabilized insulin by increasing its α-helical content. GLAE inhibited the mammalian α-glucosidase (IC
    MeSH term(s) Animals ; Humans ; alpha-Glucosidases/metabolism ; Glycosides/analysis ; Gymnema ; Insulins/analysis ; Molecular Docking Simulation ; Phytochemicals/pharmacology ; Plant Extracts/chemistry ; Plant Leaves/chemistry ; Tandem Mass Spectrometry
    Chemical Substances alpha-Glucosidases (EC 3.2.1.20) ; Glycosides ; Insulins ; Phytochemicals ; Plant Extracts
    Language English
    Publishing date 2023-09-28
    Publishing country England
    Document type Journal Article
    ISSN 1476-928X
    ISSN (online) 1476-928X
    DOI 10.1016/j.compbiolchem.2023.107964
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  7. Article: Binding mechanism of naringenin with monoamine oxidase - B enzyme: QM/MM and molecular dynamics perspective.

    Govindasamy, Hunday / Magudeeswaran, Sivanandam / Kandasamy, Saravanan / Poomani, Kumaradhas

    Heliyon

    2021  Volume 7, Issue 4, Page(s) e06684

    Abstract: The reduced level of dopamine at midbrain (substantia nigra) leads to Parkinson disease by the influence of monoamine oxidation process of monoamine oxidase B (MAO-B) enzyme. This disease mostly affects the aged people. Reports outline that the ... ...

    Abstract The reduced level of dopamine at midbrain (substantia nigra) leads to Parkinson disease by the influence of monoamine oxidation process of monoamine oxidase B (MAO-B) enzyme. This disease mostly affects the aged people. Reports outline that the naringenin molecule acts as an inhibitor of MAO-B enzyme and it potentially prevents the development of PD. To elucidate the binding mechanism of naringenin with MAO-B, we performed the molecular docking, QM/MM and molecular dynamics (MD) simulations. The molecular docking results confirm that the naringenin strongly binds with the substrate binding site of MAO-B enzyme (-12.0 kcal/mol). The low values of RMSD, RMSF and Rg indicate that the naringenin - MAO-B complex is stable over the entire period of MD simulation. Naringenin forms strong interaction with the orient keeper residue Tyr326 and other binding site residues Leu171, Glu206 and these interactions were maintained throughout the MD simulation. It is also important to block the function of MAO-B enzyme. The QM/MM study coupled with the charge density analysis reveals the charge density distribution and the strength of intermolecular interactions of naringenin-MAO-B complex. The above results suggest that this molecule is a potential inhibitor of MAO-B enzyme.
    Language English
    Publishing date 2021-04-08
    Publishing country England
    Document type Journal Article
    ZDB-ID 2835763-2
    ISSN 2405-8440
    ISSN 2405-8440
    DOI 10.1016/j.heliyon.2021.e06684
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  8. Article ; Online: Dynamics and binding affinity of nucleoside and non-nucleoside inhibitors with RdRp of SARS-CoV-2: a molecular screening, docking, and molecular dynamics simulation study.

    Chinnamadhu, Archana / Ramakrishnan, Jaganathan / Suresh, Suganya / Ramadurai, Prakash / Poomani, Kumaradhas

    Journal of biomolecular structure & dynamics

    2022  Volume 41, Issue 20, Page(s) 10396–10410

    Abstract: In this COVID-19 pandemic situation, an appropriate drug is urgent to fight against this infectious disease to save lives and prevent mortality. Repurposed drugs and vaccines are the immediate solutions for this medical emergency until discover a new ... ...

    Abstract In this COVID-19 pandemic situation, an appropriate drug is urgent to fight against this infectious disease to save lives and prevent mortality. Repurposed drugs and vaccines are the immediate solutions for this medical emergency until discover a new drug to treat this disease. As of now, no specific drug is available to cure this disease completely. Several drug targets were identified in SARS-CoV-2, in which RdRp protein is one of the potential targets to inhibit this virus infection.
    MeSH term(s) Humans ; SARS-CoV-2 ; Molecular Dynamics Simulation ; COVID-19 ; Nucleosides/pharmacology ; Molecular Docking Simulation ; Pandemics ; Amino Acids ; RNA-Dependent RNA Polymerase ; Antiviral Agents/pharmacology
    Chemical Substances Nucleosides ; Amino Acids ; RNA-Dependent RNA Polymerase (EC 2.7.7.48) ; Antiviral Agents
    Language English
    Publishing date 2022-12-12
    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 10.1080/07391102.2022.2154844
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  9. Article ; Online: Binding mechanism of spinosine and venenatine molecules with p300 HAT enzyme: Molecular screening, molecular dynamics and free-energy analysis.

    Magudeeswaran, Sivanandam / Poomani, Kumaradhas

    Journal of cellular biochemistry

    2019  Volume 121, Issue 2, Page(s) 1759–1777

    Abstract: The chromatin modification is regulated by the histone acetyltransferase (HAT) and histone deacetyltransferase (HDAC) enzymes; abnormal function of these enzymes leads to several malignant diseases. The inhibition of these enzymes using natural ligand ... ...

    Abstract The chromatin modification is regulated by the histone acetyltransferase (HAT) and histone deacetyltransferase (HDAC) enzymes; abnormal function of these enzymes leads to several malignant diseases. The inhibition of these enzymes using natural ligand molecules is an emerging technique to cure these diseases. The in vitro analysis of natural molecules, venenatine, spinosine, palmatine and taxodione are giving the best inhibition rate against p300 HAT enzyme. However, the detailed understanding of binding and the stability of these molecules with p300 HAT is not yet known. The aim of the present study is focused to determine the binding strength of the molecules from molecular dynamics simulation analysis. The docking analysis confirms that, the venenatine (-6.97 kcal/mol - conformer 8), spinosine (-6.52 kcal/mol conformer -10), palmatine (-5.72 kcal/mol conformer-3) and taxodione (-4.99 kcal/mol conformer-4) molecules form strong hydrogen bonding interactions with the key amino acid residues (Arg1410, Thr1411 and Trp1466) present in the active site of p300. In the molecular dynamics (MD) simulation, the spinosine retain these key interactions with the active site amino acid residues (Arg1410, Thr1411, and Trp1466) than venenatine and are stable throughout the simulation. The RMSD value of spinosine (0.5 to 1.3 Å) and venenatine (0.3 to 1.3 Å) are almost equal during the MD simulation. However, during the MD simulation, the intermolecular interaction between venenatine and the active site amino acid residues (Arg1410, Thr1411, and Trp1466) decreased on comparing with the spinosine-p300 interaction. The binding free energy of the spinosine (-15.30 kcal/mol) is relatively higher than the venenatine (-11.8 kcal/mol); this increment is attributed to the strong hydrogen bonding interactions of spinosine molecule with the active site amino acid residues of p300.
    MeSH term(s) Alkaloids/chemistry ; Alkaloids/metabolism ; Berberine Alkaloids/chemistry ; Berberine Alkaloids/metabolism ; Catalytic Domain ; Crystallography, X-Ray ; Enzyme Stability ; Humans ; Models, Molecular ; Molecular Dynamics Simulation ; p300-CBP Transcription Factors/chemistry ; p300-CBP Transcription Factors/metabolism
    Chemical Substances Alkaloids ; Berberine Alkaloids ; spinosine ; venenatine (1055-75-0) ; p300-CBP Transcription Factors (EC 2.3.1.48)
    Language English
    Publishing date 2019-10-21
    Publishing country United States
    Document type Journal Article
    ZDB-ID 392402-6
    ISSN 1097-4644 ; 0730-2312
    ISSN (online) 1097-4644
    ISSN 0730-2312
    DOI 10.1002/jcb.29412
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  10. Article ; Online: Insights on structure and interactions of 2-amino-4-methoxy-6-methylpyrimidinium salts with 4-aminosalicylate and 5-chlorosalicylate: a combined experimental and theoretical charge-density analysis.

    Suresh, Suganya / Kandasamy, Saravanan / Balasubramanian, Hemalatha / Ramakrishnan, Jaganathan / Poomani, Kumaradhas

    Acta crystallographica. Section C, Structural chemistry

    2022  Volume 78, Issue Pt 3, Page(s) 181–191

    Abstract: The proton-transfer complexes 2-amino-4-methoxy-6-methylpyrimidinium (2A4M6MP) 4-aminosalicylate (4AMSA), ... ...

    Abstract The proton-transfer complexes 2-amino-4-methoxy-6-methylpyrimidinium (2A4M6MP) 4-aminosalicylate (4AMSA), C
    MeSH term(s) Crystallography, X-Ray ; Hydrogen Bonding ; Quantum Theory ; Salicylates ; Salts
    Chemical Substances Salicylates ; Salts ; 5-chlorosalicylic acid (J2YFG68VCZ)
    Language English
    Publishing date 2022-02-14
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2025703-X
    ISSN 2053-2296 ; 1600-5759 ; 0108-2701
    ISSN (online) 2053-2296 ; 1600-5759
    ISSN 0108-2701
    DOI 10.1107/S2053229622001280
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