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Article ; Online: Amelioration of Amyloid-β Induced Alzheimer's Disease by Bacopa monnieri through Modulation of Mitochondrial Dysfunction and GSK-3β/Wnt/β-Catenin Signaling.

Sushma / Sahu, Manas Ranjan / Murugan, Natarajan Arul / Mondal, Amal Chandra

2023 , Page(s) e2300245

Abstract: Background: Alzheimer's disease (AD) is the most prevalent dementia, affecting a large number of populations. Despite being under scrutiny for decades, an effective therapeutic option is still not available.: Methods and results: This study explores ... ...

Abstract	Background: Alzheimer's disease (AD) is the most prevalent dementia, affecting a large number of populations. Despite being under scrutiny for decades, an effective therapeutic option is still not available. Methods and results: This study explores the therapeutic role of a nootropic herb Bacopa monnieri (BM) in AD-like pathological conditions produced by injecting preformed amyloid-β Conclusion: BM has been used in diet as a nootropic herb for several centuries. This study highlights the anti-Alzheimer activity of BM from the behavioral to the molecular level by modulating mitochondrial dysfunction, and GSK-3β mediates the Wnt/β-catenin signaling pathway.
Language	English
Publishing date	2023-12-24
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2160372-8
ISSN	1613-4133 ; 1613-4125
ISSN (online)	1613-4133
ISSN	1613-4125
DOI	10.1002/mnfr.202300245
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Article ; Online: Spontaneous nanoemulsification of cinnamon essential oil: Formulation, characterization, and antibacterial and antibiofilm activity against fish spoilage caused by Serratia rubidaea BFMO8.

Arul Raj, Jasmin Suriya / Aliyas, Sheena / Poomany Arul Soundara Rajan, Yolin Angel / Murugan, Kasi / Karuppiah, Ponmurugan / Arumugam, Natarajan / Almansour, Abdulrahman I / Karthikeyan, Perumal

Biotechnology and applied biochemistry

2024

Abstract: The contemporary food industry's uses of nanoemulsions (NEs) include food processing, effective nutraceutical delivery, the development of functional chemicals, and the synthesis of natural preservatives, such as phytocompounds. Although cinnamon ... ...

Abstract	The contemporary food industry's uses of nanoemulsions (NEs) include food processing, effective nutraceutical delivery, the development of functional chemicals, and the synthesis of natural preservatives, such as phytocompounds. Although cinnamon essential oil (CEO) is widely used in the cosmetic, pharmaceutical, and food industries, it is difficult to add to aqueous-based food formulations due to its weak stability and poor water solubility. This study describes the formulation of a CEO nanoemulsion (CEONE) by spontaneous emulsification and evaluates its antibacterial and antibiofilm properties against biofilm-forming Serratia rubidaea BFMO8 isolated from spoiled emperor fish (Lethrinus miniatus). Bacteria causing spoilage in emperor fish were isolated and identified as S. rubidaea using common morphological, cultural, and 16S RNA sequencing methods, and their ability to form biofilms and their susceptibility to CEONE were assessed using biofilm-specific methods. The spontaneous emulsification formulation of CEONE was accomplished using water and Tween 20 surfactant by manipulating organic and aqueous phase interface properties and controlling particle growth by capping surfactant increases. The best emulsification, with highly stable nano-size droplets, was accomplished at 750 rpm and a 1:3 ratio concentration. The stable CEONE droplet size, polydispersity index, and zeta potential values were 204.8 nm, 0.115, and -6.05 mV, respectively. FTIR and high-resolution liquid chromatography-mass spectrometry (HR-LCMS) analyses have revealed carboxyl, carbonyl, and phenol-like primary phytochemical functional groups in CEO and CEONE, which contribute to their antibacterial and antibiofilm properties.
Language	English
Publishing date	2024-01-22
Publishing country	United States
Document type	Journal Article
ZDB-ID	883433-7
ISSN	1470-8744 ; 0885-4513
ISSN (online)	1470-8744
ISSN	0885-4513
DOI	10.1002/bab.2555
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Article ; Online: Diet-induced animal model anti-obesity, phytochemical profiling, and

Jeyakumar, Palanisamy / Jasmin Suriya, Arul Raj / Yolin Angel, Poomany Arul Soundara Rajan / Mangala Nagasundari, Sivasubbu / Natarajan, Parathesia Pillai / Murugan, Kasi

Journal of biomolecular structure & dynamics

2023 , Page(s) 1–16

Abstract: Plant-based diets (PBDs) are renowned for managing and developing bioactive chemical inhibitors to combat obesity, a well-known global public health concern. There are currently no published research studies examining the effects of food plant mucilage ... ...

Abstract	Plant-based diets (PBDs) are renowned for managing and developing bioactive chemical inhibitors to combat obesity, a well-known global public health concern. There are currently no published research studies examining the effects of food plant mucilage dietary supplements on animal models of obesity induced by high-fat diets (HFD). The present research investigated the anti-obesity properties of the culinary plant
Language	English
Publishing date	2023-10-30
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2274516
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Article ; Online: Improved Binding Affinity of Omicron’s Spike Protein for the Human Angiotensin-Converting Enzyme 2 Receptor Is the Key behind Its Increased Virulence

Rajender Kumar / Natarajan Arul Murugan / Vaibhav Srivastava

International Journal of Molecular Sciences, Vol 23, Iss 3409, p

2022 Volume 3409

Abstract: The new variant of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), Omicron, has been quickly spreading in many countries worldwide. Compared to the original virus, Omicron is characterized by several mutations in its genomic region, ... ...

Abstract	The new variant of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), Omicron, has been quickly spreading in many countries worldwide. Compared to the original virus, Omicron is characterized by several mutations in its genomic region, including the spike protein’s receptor-binding domain (RBD). We have computationally investigated the interaction between the RBD of both the wild type and Omicron variant of SARS-CoV-2 with the human angiotensin-converting enzyme 2 (hACE2) receptor using molecular dynamics and molecular mechanics-generalized Born surface area (MM-GBSA)-based binding free energy calculations. The mode of the interaction between Omicron’s RBD with the hACE2 receptor is similar to the original SARS-CoV-2 RBD except for a few key differences. The binding free energy difference shows that the spike protein of Omicron has an increased affinity for the hACE2 receptor. The mutated residues in the RBD showed strong interactions with a few amino acid residues of hACE2. More specifically, strong electrostatic interactions (salt bridges) and hydrogen bonding were observed between R493 and R498 residues of the Omicron RBD with D30/E35 and D38 residues of the hACE2, respectively. Other mutated amino acids in the Omicron RBD, e.g., S496 and H505, also exhibited hydrogen bonding with the hACE2 receptor. A pi-stacking interaction was also observed between tyrosine residues (RBD-Tyr501: hACE2-Tyr41) in the complex, which contributes majorly to the binding free energies and suggests that this is one of the key interactions stabilizing the formation of the complex. The resulting structural insights into the RBD:hACE2 complex, the binding mode information within it, and residue-wise contributions to the free energy provide insight into the increased transmissibility of Omicron and pave the way to design and optimize novel antiviral agents.
Keywords	severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) ; Omicron ; human angiotensin-converting enzyme 2 (hACE2) ; molecular dynamics simulation ; receptor-binding domain (RBD) ; receptor-binding motif (RBM) ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	540
Language	English
Publishing date	2022-03-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
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Article ; Online: Improved Binding Affinity of Omicron's Spike Protein for the Human Angiotensin-Converting Enzyme 2 Receptor Is the Key behind Its Increased Virulence.

Kumar, Rajender / Murugan, Natarajan Arul / Srivastava, Vaibhav

International journal of molecular sciences

2022 Volume 23, Issue 6

Abstract	The new variant of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), Omicron, has been quickly spreading in many countries worldwide. Compared to the original virus, Omicron is characterized by several mutations in its genomic region, including the spike protein's receptor-binding domain (RBD). We have computationally investigated the interaction between the RBD of both the wild type and Omicron variant of SARS-CoV-2 with the human angiotensin-converting enzyme 2 (hACE2) receptor using molecular dynamics and molecular mechanics-generalized Born surface area (MM-GBSA)-based binding free energy calculations. The mode of the interaction between Omicron's RBD with the hACE2 receptor is similar to the original SARS-CoV-2 RBD except for a few key differences. The binding free energy difference shows that the spike protein of Omicron has an increased affinity for the hACE2 receptor. The mutated residues in the RBD showed strong interactions with a few amino acid residues of hACE2. More specifically, strong electrostatic interactions (salt bridges) and hydrogen bonding were observed between R493 and R498 residues of the Omicron RBD with D30/E35 and D38 residues of the hACE2, respectively. Other mutated amino acids in the Omicron RBD, e.g., S496 and H505, also exhibited hydrogen bonding with the hACE2 receptor. A pi-stacking interaction was also observed between tyrosine residues (RBD-Tyr501: hACE2-Tyr41) in the complex, which contributes majorly to the binding free energies and suggests that this is one of the key interactions stabilizing the formation of the complex. The resulting structural insights into the RBD:hACE2 complex, the binding mode information within it, and residue-wise contributions to the free energy provide insight into the increased transmissibility of Omicron and pave the way to design and optimize novel antiviral agents.
MeSH term(s)	Angiotensin-Converting Enzyme 2 ; COVID-19 ; Humans ; Protein Binding ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus/metabolism ; Virulence
Chemical Substances	Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; ACE2 protein, human (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Language	English
Publishing date	2022-03-21
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms23063409
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Article ; Online: Discovery of biphenyl pyrazole scaffold for neurodegenerative diseases: A novel class of acetylcholinesterase-centered multitargeted ligands.

Gabr, Moustafa / Murugan, Natarajan Arul

Bioorganic & medicinal chemistry letters

2020 Volume 30, Issue 17, Page(s) 127370

Abstract: Multitargeted ligands have demonstrated remarkable efficiency as potential therapeutics for neurodegenerative diseases as they target multiple pathways involved in the progression of these diseases. Herein, we report first-in-class dual inhibitor of ... ...

Abstract	Multitargeted ligands have demonstrated remarkable efficiency as potential therapeutics for neurodegenerative diseases as they target multiple pathways involved in the progression of these diseases. Herein, we report first-in-class dual inhibitor of acetylcholinesterase (AChE) and tau aggregation as a novel class of multitargeted ligands for neurodegenerative diseases. The reported biphenyl pyrazole scaffold binds monomeric tau with submicromolar affinity and impedes the formation of tau oligomers at early stages. Additionally, the lead compound inhibited AChE activity with an IC
MeSH term(s)	Acetylcholinesterase/chemistry ; Acetylcholinesterase/metabolism ; Binding Sites ; Blood-Brain Barrier/drug effects ; Blood-Brain Barrier/metabolism ; Cell Line, Tumor ; Cell Survival/drug effects ; Cholinesterase Inhibitors/chemistry ; Cholinesterase Inhibitors/pharmacology ; Cholinesterase Inhibitors/therapeutic use ; Drug Design ; Humans ; Ligands ; Molecular Docking Simulation ; Neurodegenerative Diseases/drug therapy ; Neurodegenerative Diseases/pathology ; Neuroprotective Agents/chemistry ; Neuroprotective Agents/pharmacology ; Neuroprotective Agents/therapeutic use ; Protein Aggregates/drug effects ; Pyrazoles/chemistry ; Pyrazoles/pharmacology ; Pyrazoles/therapeutic use ; tau Proteins/antagonists & inhibitors ; tau Proteins/metabolism
Chemical Substances	Cholinesterase Inhibitors ; Ligands ; Neuroprotective Agents ; Protein Aggregates ; Pyrazoles ; tau Proteins ; Acetylcholinesterase (EC 3.1.1.7)
Language	English
Publishing date	2020-07-15
Publishing country	England
Document type	Journal Article
ZDB-ID	1063195-1
ISSN	1464-3405 ; 0960-894X
ISSN (online)	1464-3405
ISSN	0960-894X
DOI	10.1016/j.bmcl.2020.127370
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Article ; Online: Assessment of Amyloid Forming Tendency of Peptide Sequences from Amyloid Beta and Tau Proteins Using Force-Field, Semi-Empirical, and Density Functional Theory Calculations

Charuvaka Muvva / Natarajan Arul Murugan / Venkatesan Subramanian

International Journal of Molecular Sciences, Vol 22, Iss 3244, p

2021 Volume 3244

Abstract: A wide variety of neurodegenerative diseases are characterized by the accumulation of protein aggregates in intraneuronal or extraneuronal brain regions. In Alzheimer’s disease (AD), the extracellular aggregates originate from amyloid-β proteins, while ... ...

Abstract	A wide variety of neurodegenerative diseases are characterized by the accumulation of protein aggregates in intraneuronal or extraneuronal brain regions. In Alzheimer’s disease (AD), the extracellular aggregates originate from amyloid-β proteins, while the intracellular aggregates are formed from microtubule-binding tau proteins. The amyloid forming peptide sequences in the amyloid-β peptides and tau proteins are responsible for aggregate formation. Experimental studies have until the date reported many of such amyloid forming peptide sequences in different proteins, however, there is still limited molecular level understanding about their tendency to form aggregates. In this study, we employed umbrella sampling simulations and subsequent electronic structure theory calculations in order to estimate the energy profiles for interconversion of the helix to β-sheet like secondary structures of sequences from amyloid-β protein (KLVFFA) and tau protein (QVEVKSEKLD and VQIVYKPVD). The study also included a poly-alanine sequence as a reference system. The calculated force-field based free energy profiles predicted a flat minimum for monomers of sequences from amyloid and tau proteins corresponding to an α-helix like secondary structure. For the parallel and anti-parallel dimer of KLVFFA, double well potentials were obtained with the minima corresponding to α-helix and β-sheet like secondary structures. A similar double well-like potential has been found for dimeric forms for the sequences from tau fibril. Complementary semi-empirical and density functional theory calculations displayed similar trends, validating the force-field based free energy profiles obtained for these systems.
Keywords	Alzheimer’s disease ; amyloid-β peptide ; amyloid forming peptides ; Tau protein ; umbrella sampling simulations ; free energy calculations ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	612
Language	English
Publishing date	2021-03-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Assessment of Amyloid Forming Tendency of Peptide Sequences from Amyloid Beta and Tau Proteins Using Force-Field, Semi-Empirical, and Density Functional Theory Calculations.

Muvva, Charuvaka / Murugan, Natarajan Arul / Subramanian, Venkatesan

International journal of molecular sciences

2021 Volume 22, Issue 6

Abstract: A wide variety of neurodegenerative diseases are characterized by the accumulation of protein aggregates in intraneuronal or extraneuronal brain regions. In Alzheimer's disease (AD), the extracellular aggregates originate from amyloid-β proteins, while ... ...

Abstract	A wide variety of neurodegenerative diseases are characterized by the accumulation of protein aggregates in intraneuronal or extraneuronal brain regions. In Alzheimer's disease (AD), the extracellular aggregates originate from amyloid-β proteins, while the intracellular aggregates are formed from microtubule-binding tau proteins. The amyloid forming peptide sequences in the amyloid-β peptides and tau proteins are responsible for aggregate formation. Experimental studies have until the date reported many of such amyloid forming peptide sequences in different proteins, however, there is still limited molecular level understanding about their tendency to form aggregates. In this study, we employed umbrella sampling simulations and subsequent electronic structure theory calculations in order to estimate the energy profiles for interconversion of the helix to β-sheet like secondary structures of sequences from amyloid-β protein (KLVFFA) and tau protein (QVEVKSEKLD and VQIVYKPVD). The study also included a poly-alanine sequence as a reference system. The calculated force-field based free energy profiles predicted a flat minimum for monomers of sequences from amyloid and tau proteins corresponding to an α-helix like secondary structure. For the parallel and anti-parallel dimer of KLVFFA, double well potentials were obtained with the minima corresponding to α-helix and β-sheet like secondary structures. A similar double well-like potential has been found for dimeric forms for the sequences from tau fibril. Complementary semi-empirical and density functional theory calculations displayed similar trends, validating the force-field based free energy profiles obtained for these systems.
MeSH term(s)	Amino Acid Sequence ; Amyloid/chemistry ; Amyloid/metabolism ; Amyloid beta-Peptides/chemistry ; Amyloid beta-Peptides/metabolism ; Density Functional Theory ; Humans ; Intrinsically Disordered Proteins/chemistry ; Intrinsically Disordered Proteins/metabolism ; Models, Molecular ; Peptide Fragments/chemistry ; Peptide Fragments/metabolism ; Protein Conformation ; Protein Conformation, alpha-Helical ; Structure-Activity Relationship ; tau Proteins/chemistry ; tau Proteins/metabolism
Chemical Substances	Amyloid ; Amyloid beta-Peptides ; Intrinsically Disordered Proteins ; Peptide Fragments ; tau Proteins
Language	English
Publishing date	2021-03-23
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms22063244
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Article ; Online: Computational investigation on

Murugan, Natarajan Arul / Pandian, Chitra Jeyaraj / Jeyakanthan, Jeyaraman

Journal of biomolecular structure & dynamics

2020 Volume 39, Issue 12, Page(s) 4415–4426

Abstract: The outbreak due to SARS-CoV-2 (or Covid-19) is spreading alarmingly and number of deaths due to infection is aggressively increasing every day. Due to the rapid human to human transmission of Covid-19, we are in need to find a potent drug at the ... ...

Abstract	The outbreak due to SARS-CoV-2 (or Covid-19) is spreading alarmingly and number of deaths due to infection is aggressively increasing every day. Due to the rapid human to human transmission of Covid-19, we are in need to find a potent drug at the earliest by ruling-out the traditional time-consuming approach of drug development. This is only possible if we use reliable computational approaches for screening compounds from chemical space or by drug repurposing or by finding the phytochemicals and nutraceuticals from plants as they can be immediately used without the need for carrying out drug-trials to test safety and efficacy. A number of plant products were routinely suggested as drugs in traditional Indian and Chinese medicine. Here using molecular docking approach, and combined molecular dynamics and MM-GBSA based free energy calculations approach, we study the potency of the four selected phytochemicals namely andrographolide (AGP1), 14-deoxy 11,12-didehydro andrographolide (AGP2), neoandrographolide (AGP3) and 14-deoxy andrographolide (AGP4) from
MeSH term(s)	Andrographis ; Antiviral Agents/pharmacology ; COVID-19 ; Humans ; Molecular Docking Simulation ; Pharmaceutical Preparations ; Phytochemicals/pharmacology ; SARS-CoV-2
Chemical Substances	Antiviral Agents ; Pharmaceutical Preparations ; Phytochemicals
Keywords	covid19
Language	English
Publishing date	2020-06-16
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	10.1080/07391102.2020.1777901
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Article: A Review on Parallel Virtual Screening Softwares for High-Performance Computers.

Murugan, Natarajan Arul / Podobas, Artur / Gadioli, Davide / Vitali, Emanuele / Palermo, Gianluca / Markidis, Stefano

Pharmaceuticals (Basel, Switzerland)

2022 Volume 15, Issue 1

Abstract: Drug discovery is the most expensive, time-demanding, and challenging project in biopharmaceutical companies which aims at the identification and optimization of lead compounds from large-sized chemical libraries. The lead compounds should have high- ... ...

Abstract	Drug discovery is the most expensive, time-demanding, and challenging project in biopharmaceutical companies which aims at the identification and optimization of lead compounds from large-sized chemical libraries. The lead compounds should have high-affinity binding and specificity for a target associated with a disease, and, in addition, they should have favorable pharmacodynamic and pharmacokinetic properties (grouped as ADMET properties). Overall, drug discovery is a multivariable optimization and can be carried out in supercomputers using a reliable scoring function which is a measure of binding affinity or inhibition potential of the drug-like compound. The major problem is that the number of compounds in the chemical spaces is huge, making the computational drug discovery very demanding. However, it is cheaper and less time-consuming when compared to experimental high-throughput screening. As the problem is to find the most stable (global) minima for numerous protein-ligand complexes (on the order of 106 to 1012), the parallel implementation of in silico virtual screening can be exploited to ensure drug discovery in affordable time. In this review, we discuss such implementations of parallelization algorithms in virtual screening programs. The nature of different scoring functions and search algorithms are discussed, together with a performance analysis of several docking softwares ported on high-performance computing architectures.
Language	English
Publishing date	2022-01-04
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2193542-7
ISSN	1424-8247
ISSN	1424-8247
DOI	10.3390/ph15010063
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