Drug–target affinity prediction using graph neural network and contact maps

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ADME profiling, molecular docking, DFT, and MEP analysis reveal cissamaline, cissamanine, and cissamdine from Cissampelos capensis L.f. as potential anti-Alzheimer's agents

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3D‐QSAR‐Based Pharmacophore Modeling, Virtual Screening, and Molecular Docking Studies for Identification of Tubulin Inhibitors with Potential Anticancer Activity

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BioMed Research International, 2021, 2021
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Combined machine learning and pharmacophore based virtual screening approaches to screen for antibiofilm inhibitors targeting LasR of Pseudomonas aeruginosa

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Journal of Biomolecular Structure and Dynamics, 2023, 41, 4124
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Evaluating Iso-Mukaadial Acetate and Ursolic Acid Acetate as Plasmodium falciparum Hypoxanthine-Guanine-Xanthine Phosphoribosyltransferase Inhibitors

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Integrating multi-structure covalent docking with machine-learning consensus scoring enhances potency ranking of human acetylcholinesterase inhibitors

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Identification of novel inhibitors targeting EGFR L858R/T790M/C797S against NSCLC by molecular docking, MD simulation, and DFT approaches

Chaochun Wei, Cuicui Ji, Keli Zong, Xiaokun Zhang, Qidi Zhong, Hong Yan and Juan Wang

Journal of Molecular Graphics and Modelling, 2025, 138, 109052
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Development of homology model, docking protocol and Machine-Learning based scoring functions for identification of Equus caballus’s butyrylcholinesterase inhibitors

Ankit Ganeshpurkar, Ravi Singh, Devendra Kumar, Gopichand Gutti, Divya Sardana, Shalini Shivhare, Ravi Bhushan Singh, Ashok Kumar and Sushil Kumar Singh

Journal of Biomolecular Structure and Dynamics, 2022, 40, 13693
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Machine intelligence-guided selection of optimized inhibitor for human immunodeficiency virus (HIV) from natural products

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Machine learning models for drug–target interactions: current knowledge and future directions

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Spike protein recognizer receptor ACE2 targeted identification of potential natural antiviral drug candidates against SARS-CoV-2

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International Journal of Biological Macromolecules, 2021, 191, 1114
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Therapeutic potential of Chromolaena odorata phyto-constituents against human pancreatic α-amylase

Babatomiwa Kikiowo, Joseph A. Ogunleye, Opeyemi Iwaloye and Taiwo T. Ijatuyi

Journal of Biomolecular Structure and Dynamics, 2022, 40, 1801
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Identification of novel SARS-CoV-2 3CLpro inhibitors by molecular docking, in vitro assays, molecular dynamics simulations and DFT analyses

Keli Zong, Chaochun Wei, Wei Li, Jiajun Ruan, Susu Zhang, Jingjing Li, Xiaojing Liu, Xu Zhao, Ruiyuan Cao, Hong Yan and Xingzhou Li

Front. Pharmacol., 2024, 15
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Uncovering plant-derived compounds to treat Alzheimer's disease by targeting the acetylcholinesterase enzyme through computational studies

Al Riyad Hasan, Sohel Rana, Alok Kumer, Nazmul Hossain, Sabekun Nahar Sezin, Md. Tarikul Islam, Nazim Uddin Molla, Md. Nazir Hosen, Nusrat Mahjabin Maha, Marzia Mahzabin Mahi, Symon Saroar, Md. Aktaruzzaman and Md. Obayed Raihan

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Thioredoxin system in colorectal cancer: Its role in carcinogenesis, disease progression, and response to treatment

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Life Sciences, 2024, 348, 122711
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Antioxidant, antiproliferative, and acetylcholinesterase inhibition activity of amino alcohol derivatives from 1,4-naphthoquinone

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Generation of wild-type rat Glucocerebrosidase homology modeling: Identification of putative interactions site and mechanism for chaperone using combined in-silico and in-vitro studies

Pratigya Tripathi, Ankit Ganeshpurkar, Sushil Kumar Singh and Sairam Krishnamurthy

Bioorganic Chemistry, 2022, 126, 105871
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4-Phthalimidobenzenesulfonamide Derivatives as Acetylcholinesterase and Butyrylcholinesterase Inhibitors: DFTs, 3D-QSAR, ADMET, and Molecular Dynamics Simulation

Syeda Abida Ejaz, Ammara Fayyaz, Hafiz Mohammad Kashif Mahmood, Mubashir Aziz, Syeda Rabia Ejaz, Afrah Fahad Alkhuriji, Wafa Abdullah I. Al-Megrin, Abdullahi Tunde Aborode and Gaber El-Saber Batiha

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Identification of natural product as selective PI3Kα inhibitor against NSCLC: multi-ligand pharmacophore modeling, molecular docking, ADME, DFT, and MD simulations

Debojyoti Halder, Subham Das and R. S. Jeyaprakash

Mol Divers, 2024, 28, 2983
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Gains from no real PAINS: Where ‘Fair Trial Strategy’ stands in the development of multi-target ligands

Jianbo Sun, Hui Zhong, Kun Wang, Na Li and Li Chen

Acta Pharmaceutica Sinica B, 2021, 11, 3417
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Use of connectivity index and simple topological parameters for estimating the inhibition potency of acetylcholinesterase

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Saudi Pharmaceutical Journal, 2022, 30, 369
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Computational Design of Novel Tau-Tubulin Kinase 1 Inhibitors for Neurodegenerative Diseases

Shahzaib Ahamad, Iqbal Taliy Junaid and Dinesh Gupta

Pharmaceuticals, 2024, 17, 952
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ELIXIR-A: An Interactive Visualization Tool for Multi-Target Pharmacophore Refinement

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ACS Omega, 2022, 7, 12707
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Identification of novel glucocerebrosidase chaperone for potential treatment of Parkinson's disease: An approach using in silico virtual screening, molecular docking and molecular dynamics, and in vitro studies

Pratigya Tripathi, Ankit Ganeshpurkar, Sushil Kumar Singh and Sairam Krishnamurthy

International Journal of Biological Macromolecules, 2023, 228, 453
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Computational Investigation on Natural Quinazoline Alkaloids as Potential Inhibitors of the Main Protease (Mpro) of SARS-CoV-2

Abhisek Jana, Tarun Roy, Sarbajit Layek, Subhas Ghosal and Deb Ranjan Banerjee

J. Comput. Biophys. Chem., 2022, 21, 65
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Structural Investigations of Aroylindole Derivatives through 3D-QSAR and Multiple Pharmacophore Modeling for the Search of Novel Colchicines Inhibitor

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LDDD, 2021, 18, 131
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The use of global and local reactivity descriptors of conceptual DFT to describe toxicity of benzoic acid derivatives

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Design, Synthesis, and Biological Evaluation of New Substituted 5‐Aryl‐Oxadiazole‐based Derivatives as Acetylcholinesterase and Butyrylcholinesterase Inhibitors

Elahe Hadadianpour, Maryam Abbasi and Behjat Pouramiri

Chemistry & Biodiversity, 2025, 22
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RETRACTED: Development of a simple QSAR model for reliable evaluation of acetylcholinesterase inhibitor potency

Ante Miličević and Goran Šinko

European Journal of Pharmaceutical Sciences, 2021, 160, 105757
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Investigation of Newly Synthesized Fluorinated Isatin-Hydrazones by In Vitro Antiproliferative Activity, Molecular Docking, ADME Analysis, and e-Pharmacophore Modeling

Eyüp Başaran, Semiha Köprü, Senem Akkoç and Burçin Türkmenoğlu

ACS Omega, 2024, 9, 26503
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Molecular dynamics simulation and pharmacokinetics studies of ombuin and quercetin against human pancreatic α-amylase

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Journal of Biomolecular Structure and Dynamics, 2023, 41, 10388
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Identifying potential GluN2B subunit containing N-Methyl-D-aspartate receptor inhibitors: an integrative in silico and molecular modeling approach

Ravi Singh, Ankit Ganeshpurkar, Devendra Kumar, Dileep Kumar, Ashok Kumar and Sushil Kumar Singh

Journal of Biomolecular Structure and Dynamics, 2020, 38, 2533
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Identification of Sulfonamide-Based Butyrylcholinesterase Inhibitors Using Machine Learning

Ankit Ganeshpurkar, Ravi Singh, Devendra Kumar, Gopichand Gutti, Pravin Gore, Bharat Sahu, Ashok Kumar and Sushil Kumar Singh

Future Med. Chem., 2022, 14, 1049
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Exploring the Thioredoxin System as a Therapeutic Target in Cancer: Mechanisms and Implications

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Design, Synthesis, and Biological andIn SilicoStudy of Fluorine‐Containing Quinoline Hybrid Thiosemicarbazide Analogues

Dhaval B. Patel, Kinjal D. Patel, Neelam P. Prajapati, Krupa R. Patel, Dhanji P. Rajani, Smita D. Rajani, Naumita S. Shah, Devendra D. Zala and Hitesh D. Patel

Journal of Heterocyclic Chem, 2019, 56, 2235
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Improved machine learning scoring functions for identification of Electrophorus electricus’s acetylcholinesterase inhibitors

Ankit Ganeshpurkar, Ravi Singh, Shalini Shivhare, Divya, Devendra Kumar, Gopichand Gutti, Ravibhushan Singh, Ashok Kumar and Sushil Kumar Singh

Mol Divers, 2022, 26, 1455
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Identification of sulfonamide based butyrylcholinesterase inhibitors through scaffold hopping approach

Ankit Ganeshpurkar, Ravi Singh, Devendra Kumar, Pravin Gore, Shalini Shivhare, Divya Sardana, Swetha Rayala, Ashok Kumar and Sushil Kumar Singh

International Journal of Biological Macromolecules, 2022, 203, 195
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Drug-target Binding Affinity Prediction Based on Three-branched Multiscale Convolutional Neural Networks

Yaoyao Lu, Junkai Liu, Tengsheng Jiang, Zhiming Cui and Hongjie Wu

CBIO, 2023, 18, 853
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Investigating the electronic properties and reactivity of polyaniline emeraldine base functionalized with metal oxides

Rania Badry, Hanan Elhaes, Asmaa Ibrahim, Ahmed Refaat and Medhat A. Ibrahim

Sci Rep, 2024, 14
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Pharmacophore-based virtual screening, molecular docking and molecular dynamics simulations study for the identification of LIM kinase-1 inhibitors

Ravi Singh, Ankit Vyankatrao Pokle, Powsali Ghosh, Ankit Ganeshpurkar, Rayala Swetha, Sushil Kumar Singh and Ashok Kumar

Journal of Biomolecular Structure and Dynamics, 2023, 41, 6089
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Machine learning-based virtual screening and molecular modelling studies for identification of butyrylcholinesterase inhibitors as anti-Alzheimer’s agent

Ankit Ganeshpurkar, Likhit Akotkar, Devendra Kumar, Dileep Kumar and Aditya Ganeshpurkar

Journal of Biomolecular Structure and Dynamics, 2025, 43, 7319
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3‐arylcoumarins as the potential neuroprotective agents for the treatment of Alzheimer's disease by targeting monoamine oxidase: Molecular docking, 3D QSAR, and molecular dynamics simulations

Ammara Fayyaz, Syeda Abida Ejaz, Mubashir Aziz, Syeda Rabia Ejaz, Chen Li, Laith Abualigah and Aseel Smerat

Vietnam Journal of Chemistry, 2026, 64, 52
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Structure-based screening and molecular dynamics simulation studies for the identification of potential acetylcholinesterase inhibitors

Ankit Ganeshpurkar, Ravi Singh, Pravin Gangaram Gore, Devendra Kumar, Gopichand Gutti, Ashok Kumar and Sushil Kumar Singh

Molecular Simulation, 2020, 46, 169
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Pharmacophore-guided fragment-based design of novel mammalian target of rapamycin inhibitors: extra precision docking, fingerprint-based 2D and atom-based 3D-QSAR modelling

Avinash Kumar, Sudhanshu Rai, Ekta Rathi, Paridhi Agarwal and Suvarna G. Kini

Journal of Biomolecular Structure and Dynamics, 2021, 39, 1155
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Assessment of scoring functions and in silico parameters for AChE-ligand interactions as a tool for predicting inhibition potency

Goran Šinko

Chemico-Biological Interactions, 2019, 308, 216
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Computational binding study with α7 nicotinic acetylcholine receptor of Anvylic-3288: an allosteric modulator

Ankit Ganeshpurkar, Ravi Singh, Devendra Kumar, Divya, Shalini Shivhare, Ashok Kumar and Sushil Kumar Singh

Molecular Simulation, 2020, 46, 975
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In silico Screening of Pyridoxine Carbamates for Anti-Alzheimer’s Activities

Dnyaneshwar Baswar, Abha Sharma and Awanish Mishra

CNSAMC, 2021, 21, 39
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Inhibition of β-lactamase by Novel Benzothiazole-Coupled Azetidinone Derivatives: A Comprehensive Study Using an In silico and In vitro Approaches Against Multi Drug Resistant Bacteria

Gupta Dheeraj Rajesh, Abel John Koshy, Sadanand Dangari Akshay, Prarambh S. R. Dwivedi, Harsha Ashtekar, Niyas Rehman and Pankaj Kumar

J. Comput. Biophys. Chem., 2024, 23, 1145
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Glucosinolates and Indole-3-carbinol from Brassica oleracea L. as inhibitors of E. coli CdtB: insights from molecular docking, dynamics, DFT and in vitro assay

Faria Tasnim, Md. Eram Hosen, Md. Enamul Haque, Ariful Islam, Mst Naharina Nuryay, Jannatul Mawya, Najnin Akter, Delara Yesmin, Md. Mosabbir Hossain, Nilima Rahman, B. M. Mahmudul Hasan, Md. Naimul Hassan, Md. Mahmudul Islam and Md. Khalekuzzaman

In Silico Pharmacol., 2024, 12
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Discovery of novel inhibitors of dengue viral RNA-dependent RNA polymerase by molecular docking, in vitro assay, DFT, and MD simulations

Chaochun Wei, Keli Zong, Wei Li, Xu Zhao, Jiajun Ruan, Susu Zhang, Jingjing Li, Xiaojing Liu, Hong Yan, Ruiyuan Cao and Xingzhou Li

International Journal of Biological Macromolecules, 2025, 305, 141328
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Structural and mechanistic insights into 15-lipoxygenase inhibition by H1-antihistamines: Evidence from SAR, MCF-7 cell studies, DNA binding, molecular docking and MD simulations

Ayesha Momen, Deeba Nawaz, Ambar Iqbal, Naheed Riaz, Magdy M.D. Mohammed, Amany M.A. Osman, Muhammad Munawar Hayat and Muhammad Ashraf

Journal of Molecular Structure, 2026, 1364, 145766
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Investigation of 3-Phenylcoumarin Derivatives as Potential Multi-target Inhibitors for Human Cholinesterases and Monoamine oxidases: A Computational Approach

Ammara Fayyaz, Syeda Abida Ejaz, Bshra A. Alsfouk and Syeda Rabia Ejaz

Appl Biochem Biotechnol, 2024, 196, 8389
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Novel triazole-based N-Acetyl schiff bases: Synthesis, computational analysis, and acetylcholinesterase and butyrylcholinesterase inhibitory potential for Alzheimer's disease

Hilal Medetalibeyoğlu, Burak Tüzün, Abdurrahman Atalay, Ahmet Buğra Ortaakarsu, Rüya Sağlamtaş, Sevda Manap, Onur Akyıldırım and Haydar Yüksek

Journal of Molecular Structure, 2025, 1347, 143176
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Computational Identification of Novel EGFR Inhibitors Containing Substituted Pyrimidine Scaffolds Targeting T790M/L858R Mutations

Shashikant Bhandari, Kshitij Fattepure, Shital Patil, Somdatta Chaudhari, Yash Shimpi, Aditi Saundarkar, Pratik Lohakare, Milind Nikalje and Sneha Pisolkar

J Pharm Innov, 2026, 21
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Effect of sulfonamide derivatives of phenylglycine on scopolamine‐induced amnesia in rats

Ankit Ganeshpurkar, Ravi Singh, Pratigya Tripathi, Qadir Alam, Sairam Krishnamurthy, Ashok Kumar and Sushil K. Singh

Ibrain, 2023, 9, 13
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Identification of novel inhibitors targeting Mycobacterium abscessus InhA through virtual screening, docking, and molecular dynamic simulations

Munawar Abbas, Abdullah R. Alanzi, Kashif Iqbal Sahibzada, Mariyam Nawaz, Ghulam Fatima and Dong-Qing Wei

Sci Rep, 2025, 15
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Mechanistic insights into angiotensin-converting enzyme inhibition by Apium graveolens through an integrative in silico–in vitro study

Neha Singh, Ankit Ganeshpurkar, Sushil Kumar Singh and Sairam Krishnamurthy

International Journal of Biological Macromolecules, 2026, 337, 149305
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