Computational investigation of the human SOD1 mutant, Cys146Arg, that directs familial amyotrophic lateral sclerosis

E. Srinivasan and R. Rajasekaran

Mol. BioSyst., 2017, 13, 1495
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Gold nanocolloid–protein interactions and their impact on β-sheet amyloid fibril formation

Heloise R. Barros, Maria Kokkinopoulou, Izabel C. Riegel-Vidotti, Katharina Landfester and Héloïse Thérien-Aubin

RSC Adv., 2018, 8, 980
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Amyloid fibrillation of the glaucoma associated myocilin protein is inhibited by epicatechin gallate (ECG)

Ritika Sharma, Anchala Kumari, Bishwajit Kundu and Abhinav Grover

RSC Adv., 2022, 12, 29469
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Conformational dynamics of superoxide dismutase (SOD1) in osmolytes: a molecular dynamics simulation study

Ishrat Jahan and Shahid M. Nayeem

RSC Adv., 2020, 10, 27598
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Edaravone inhibits the conformational transition of amyloid-β42: insights from molecular dynamics simulations

Fufeng Liu, Zheng Ma, Jingcheng Sang and Fuping Lu

Journal of Biomolecular Structure and Dynamics, 2020, 38, 2377
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A molecular dynamics simulations study of the ionic liquid effect on the β-glucosidase active site interactions with a flavonoid glycoside

Samira Hozhabr Araghi, Amalraj John and Mohammad Sadegh Sadeghi Googheri

Journal of Molecular Liquids, 2021, 340, 117115
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A rapid in vivo pipeline to identify small molecule inhibitors of amyloid aggregation

Muntasir Kamal, Jessica Knox, Robert I. Horne, Om Shanker Tiwari, Andrew R. Burns, Duhyun Han, Davide Levy, Dana Laor Bar-Yosef, Ehud Gazit, Michele Vendruscolo and Peter J. Roy

Nat Commun, 2024, 15
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Unveiling the inhibitory mechanism of peptidomimetic inhibitor against Aβ42 aggregation and protofibril disaggregation by molecular dynamics

Rajdeep Kaur, Rajneet Kaur Saini, Pritpal Singh and Bhupesh Goyal

Journal of Molecular Liquids, 2021, 335, 116474
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Direct Interaction of Minocycline to p47phox Contributes to its Attenuation of TNF-α-Mediated Neuronal PC12 Cell Death: Experimental and Simulation Validation

Habib Eslami, Koosha Rokhzadi, Mohsen Basiri, Saeed Esmaeili-Mahani, Zahra Mahmoodi and Kaveh Haji-Allahverdipoor

Cell Biochem Biophys, 2024, 82, 1261
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Recent advances in the design and applications of amyloid-β peptide aggregation inhibitors for Alzheimer’s disease therapy

Safura Jokar, Saeedeh Khazaei, Hossein Behnammanesh, Amir Shamloo, Mostafa Erfani, Davood Beiki and Omid Bavi

Biophys Rev, 2019, 11, 901
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An in-silico study to gain a comprehensive understanding of the effects of glucosylation on quercetin properties

Samira Hozhabr Araghi, John Amalraj, Motahare Sadeghi Googheri, Radha D. Pyarasani and Mohammad Sadegh Sadeghi Googheri

Computational and Theoretical Chemistry, 2023, 1220, 113981
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Does hazelnut consumption affect brain health and function against neurodegenerative diseases?

Shadi Talebi, Fariba Khodagholi, Zahra Bahaeddin, Mitra Ansari Dezfouli, Arman Zeinaddini-Meymand, Samuel Berchi Kankam, Forough Foolad, Fatemeh Alijaniha and Fatemeh Fayazi Piranghar

Nutritional Neuroscience, 2024, 27, 1008
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Bioactive Peptides of Fermented Food Products Targeting the Structural Rigid Core of Amyloid Fibril Unravelled by Simulated Thermal Unfolding in Alzheimer’s Disorder

G. Chandrasekhar and R. Rajasekaran

Int J Pept Res Ther, 2023, 29
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Exploring Metformin’s Therapeutic Potential for Alzheimer’s Disease: An In-Silico Perspective Using Well-Tempered Funnel Metadynamics

Sunandini Swain and Atanu K. Metya

J. Chem. Inf. Model., 2025, 65, 4163
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Molecular insights into the very early steps of Aβ1-42 pentameric protofibril disassembly by PGG: A molecular dynamics simulation study

Rong-zu Nie, Shuang Cai, Bo Yu, Wen-ying Fan, Huan-huan Li, Shang-wen Tang and Yin-qiang Huo

Journal of Molecular Liquids, 2022, 361, 119638
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Alanine mutation of the catalytic sites of Pantothenate Synthetase causes distinct conformational changes in the ATP binding region

Bharati Pandey, Sonam Grover, Sukriti Goyal, Anchala Kumari, Aditi Singh, Salma Jamal, Jagdeep Kaur and Abhinav Grover

Sci Rep, 2018, 8
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Effect of osmolytes on the EcoRI endonuclease: Insights into hydration and protein dynamics from molecular dynamics simulations

Aathithya Diaz and Vigneshwar Ramakrishnan

Computational Biology and Chemistry, 2023, 105, 107883
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Insight into the inhibitor discrimination by FLT3 F691L

Sharad Verma, Aditi Singh, Anchala Kumari, Bharati Pandey, Salma Jamal, Sukriti Goyal, Siddharth Sinha and Abhinav Grover

Chem Biol Drug Des, 2018, 91, 1056
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Mobile obstacles accelerate and inhibit the bundle formation in two-patch colloidal particle

I. Malhotra and S. B. Babu

The Journal of Chemical Physics, 2019, 151
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Amentoflavone-loaded nanoparticles enhanced chemotherapy efficacy by inhibition of AKR1B10

Fang Zhao, Yumei Qian, Hongxia Li, Yang Yang, Jing Wang, Weixiong Yu, Min Li, Wei Cheng and Lingling Shan

Nanotechnology, 2022, 33, 385101
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Effects of natural compounds on conformational properties and hairpin formation of amyloid-β42 monomer: docking and molecular dynamics simulation study

Mohammad Ghorbani, Hossein Soleymani, Abdollah Allahverdi, Seyedehsamaneh Shojaeilangari and Hossein Naderi-Manesh

Journal of Biomolecular Structure and Dynamics, 2020, 38, 3371
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Molecular dynamics simulation of aluminium binding to amyloid-β and its effect on peptide structure

Matthew Turner, Shaun T. Mutter, Oliver D. Kennedy-Britten, James A. Platts and Eugene A. Permyakov

PLoS ONE, 2019, 14, e0217992
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Identification of new pentapeptides as potential inhibitors of amyloid–β42 aggregation using virtual screening and molecular dynamics simulations

Apneet Kaur and Bhupesh Goyal

Journal of Molecular Graphics and Modelling, 2023, 124, 108558
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Design, synthesis, biological evaluation, and molecular modeling studies of chalcone-rivastigmine hybrids as cholinesterase inhibitors

Ling Wang, Yu Wang, Yiguang Tian, Jinling Shang, Xiaoou Sun, Hongzhuan Chen, Hao Wang and Wen Tan

Bioorganic & Medicinal Chemistry, 2017, 25, 360
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Scrutiny of the mechanism of small molecule inhibitor preventing conformational transition of amyloid-β42 monomer: insights from molecular dynamics simulations

Suniba Shuaib and Bhupesh Goyal

Journal of Biomolecular Structure and Dynamics, 2018, 36, 663
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Novel thiophene Chalcones-Coumarin as acetylcholinesterase inhibitors: Design, synthesis, biological evaluation, molecular docking, ADMET prediction and molecular dynamics simulation

Aso Hameed Hasan, Sankaranarayanan Murugesan, Syazwani Itri Amran, Subhash Chander, Mohammed M. Alanazi, Taibi Ben Hadda, Sonam Shakya, Mohammad Rizki Fadhil Pratama, Basundhara Das, Subhrajit Biswas and Joazaizulfazli Jamalis

Bioorganic Chemistry, 2022, 119, 105572
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Molecular simulation probes the potency of resveratrol in regulating the toxic aggregation of mutant V30M TTR fibrils in Transthyretin mediated amyloidosis

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

Journal of Molecular Graphics and Modelling, 2022, 110, 108055
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How a crosslinker agent interacts with the β-glucosidase enzyme surface in an aqueous solution: Insight from quantum mechanics calculations and molecular dynamics simulations

Samira Hozhabr Araghi, Amalraj John and Mohammad Sadegh Sadeghi Googheri

Colloids and Surfaces B: Biointerfaces, 2021, 203, 111761
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Insights into the inhibitory mechanism of a resveratrol and clioquinol hybrid against Aβ42 aggregation and protofibril destabilization: A molecular dynamics simulation study

Rajneet Kaur Saini, Suniba Shuaib, Deepti Goyal and Bhupesh Goyal

Journal of Biomolecular Structure and Dynamics, 2019, 37, 3183
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Insights into the substrate binding specificity of quorum-quenching acylase PvdQ

Yanyun Liu, Jerry O. Ebalunode and James M. Briggs

Journal of Molecular Graphics and Modelling, 2019, 88, 104
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In Silico Analysis of the Antagonist Effect of Enoxaparin on the ApoE4–Amyloid-Beta (Aβ) Complex at Different pH Conditions

Jorge Alberto Aguilar-Pineda, Silvana G. Paco-Coralla, Camilo Febres-Molina, Pamela L. Gamero-Begazo, Pallavi Shrivastava, Karin J. Vera-López, Gonzalo Davila-Del-Carpio, Patricia López-C, Badhin Gómez and Christian L. Lino Cardenas

Biomolecules, 2022, 12, 499
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Insights into the Inhibitory Mechanism of Dicyanovinyl‐Substituted J147 Derivative against Aβ42 Aggregation and Protofibril Destabilization: A Molecular Dynamics Simulation Study

Suniba Shuaib, Rajneet Kaur Saini, Deepti Goyal and Bhupesh Goyal

ChemistrySelect, 2017, 2, 1645
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Insights into β-amyloid transition prevention by cucurbit[7]uril from molecular modeling

Osmair Vital de Oliveira, Arlan da Silva Gonçalves and Natália Ellen Castilho de Almeida

Journal of Biomolecular Structure and Dynamics, 2022, 40, 9602
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Structural investigations on mechanism of lapatinib resistance caused by HER-2 mutants

Sharad Verma, Sukriti Goyal, Anchala Kumari, Aditi Singh, Salma Jamal, Abhinav Grover and Anna Sapino

PLoS ONE, 2018, 13, e0190942
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Molecular insights into the inhibitory mechanisms of gallate moiety on the Aβ1–40 amyloid aggregation: A molecular dynamics simulation study

Rong-zu Nie, Yin-qiang Huo, Bo Yu, Chuan-ju Liu, Rui Zhou, Hong-hui Bao and Shang-wen Tang

International Journal of Biological Macromolecules, 2020, 156, 40
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Solid state synthesis of bispyridyl-ferrocene conjugates with unusual site selective 1,4-Michael addition, as potential inhibitor and electrochemical probe for fibrillation in amyloidogenic protein

Biplob Halder, Amit Mitra, Smriti Dewangan, Rabiul Gazi, Nandini Sarkar, Madhurima Jana and Saurav Chatterjee

Journal of Molecular Structure, 2023, 1273, 134362
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Simulations on the dual effects of flavonoids as suppressors of Aβ42 fibrillogenesis and destabilizers of mature fibrils

Sahar Andarzi Gargari and Abolfazl Barzegar

Sci Rep, 2020, 10
DOI: 10.1038/s41598-020-72734-9