Computationally driven discovery of SARS-CoV-2 Mproinhibitors: from design to experimental validation

Léa El Khoury, Zhifeng Jing, Alberto Cuzzolin, Alessandro Deplano, Daniele Loco, Boris Sattarov, Florent Hédin, Sebastian Wendeborn, Chris Ho, Dina El Ahdab, Theo Jaffrelot Inizan, Mattia Sturlese, Alice Sosic, Martina Volpiana, Angela Lugato, Marco Barone, Barbara Gatto, Maria Ludovica Macchia, Massimo Bellanda, Roberto Battistutta, Cristiano Salata, Ivan Kondratov, Rustam Iminov, Andrii Khairulin, Yaroslav Mykhalonok, Anton Pochepko, Volodymyr Chashka-Ratushnyi, Iaroslava Kos, Stefano Moro, Matthieu Montes, Pengyu Ren, Jay W. Ponder, Louis Lagardère, Jean-Philip Piquemal and Davide Sabbadin

Chem. Sci., 2022, 13, 3674
DOI: 10.1039/D1SC05892D

Spectra-descriptor-based machine learning for predicting protein–ligand interactions

Cheng Chen, Ledu Wang, Yi Feng, Wencheng Yao, Jiahe Liu, Zifan Jiang, Luyuan Zhao, Letian Zhang, Jun Jiang and Shuo Feng

Chem. Sci., 2025, 16, 6355
DOI: 10.1039/D5SC00451A

Discovery of novel tubulin polymerization inhibitors by utilizing 3D-QSAR, molecular docking and molecular dynamics simulation

Xuemin Zhao, Rui Zhang, Xiuyan Yu, Na Yu, Yuanze Shi, Mao Shu and Yan Shen

New J. Chem., 2022, 46, 16426
DOI: 10.1039/D2NJ02773A

Surely you are joking, Mr Docking!

F. Gentile, T. I. Oprea, A. Tropsha and A. Cherkasov

Chem. Soc. Rev., 2023, 52, 872
DOI: 10.1039/D2CS00948J

Automated discovery of noncovalent inhibitors of SARS-CoV-2 main protease by consensus Deep Docking of 40 billion small molecules

Francesco Gentile, Michael Fernandez, Fuqiang Ban, Anh-Tien Ton, Hazem Mslati, Carl F. Perez, Eric Leblanc, Jean Charle Yaacoub, James Gleave, Abraham Stern, Bill Wong, François Jean, Natalie Strynadka and Artem Cherkasov

Chem. Sci., 2021, 12, 15960
DOI: 10.1039/D1SC05579H

On the origins of SARS-CoV-2 main protease inhibitors

Yves L. Janin

RSC Med. Chem., 2024, 15, 81
DOI: 10.1039/D3MD00493G

Thermodynamic and structural insights into the repurposing of drugs that bind to SARS-CoV-2 main protease

Shunzhou Wan, Agastya P. Bhati, Alexander D. Wade, Dario Alfè and Peter V. Coveney

Mol. Syst. Des. Eng., 2022, 7, 123
DOI: 10.1039/D1ME00124H

Estimating the binding energetics of reversible covalent inhibitors of the SARS-CoV-2 main protease: an in silico study

Ernest Awoonor-Williams

Phys. Chem. Chem. Phys., 2022, 24, 23391
DOI: 10.1039/D2CP03080B

On drug discovery against infectious diseases and academic medicinal chemistry contributions

Yves L Janin

Beilstein J. Org. Chem., 2022, 18, 1355
DOI: 10.3762/bjoc.18.141

The role and potential of computer-aided drug discovery strategies in the discovery of novel antimicrobials

Samson O. Oselusi, Phumuzile Dube, Adeshina I. Odugbemi, Kolajo A. Akinyede, Tosin L. Ilori, Elizabeth Egieyeh, Nicole RS. Sibuyi, Mervin Meyer, Abram M. Madiehe, Gerald J. Wyckoff and Samuel A. Egieyeh

Computers in Biology and Medicine, 2024, 169, 107927
DOI: 10.1016/j.compbiomed.2024.107927

Programmable intratumoral drug delivery to breast cancer using wireless bioelectronic device with electrochemical actuation

Mohammad Souri, Sohail Elahi and Madjid Soltani

Expert Opinion on Drug Delivery, 2024, 21, 495
DOI: 10.1080/17425247.2024.2323211

Drug repositioning: lessons from the COVID-19 pandemic

VV Poroykov

Медицинская этика, 2022
DOI: 10.24075/medet.2021.027

Conserved coronavirus proteins as targets of broad-spectrum antivirals

Cleber C. Melo-Filho, Tesia Bobrowski, Holli-Joi Martin, Zoe Sessions, Konstantin I. Popov, Nathaniel J. Moorman, Ralph S. Baric, Eugene N. Muratov and Alexander Tropsha

Antiviral Research, 2022, 204, 105360
DOI: 10.1016/j.antiviral.2022.105360

Identification and Ranking of Binding Sites from Structural Ensembles: Application to SARS-CoV-2

Maria Lazou, Ayse A. Bekar-Cesaretli, Sandor Vajda and Diane Joseph-McCarthy

Viruses, 2024, 16, 1647
DOI: 10.3390/v16111647

Advances and critical assessment of machine learning techniques for prediction of docking scores

Lukas Bucinsky, Marián Gall, Ján Matúška, Michal Pitoňák and Marek Štekláč

Int J of Quantum Chemistry, 2023, 123
DOI: 10.1002/qua.27110

A novel inhibitor of SARS-CoV infection: Lactulose octasulfate interferes with ACE2-Spike protein binding

Rami Adel Pashameah, Raya Soltane and Ahmed M. Sayed

Heliyon, 2024, 10, e23222
DOI: 10.1016/j.heliyon.2023.e23222

Structural insights into the substrate‐binding site of main protease for the structure‐based COVID‐19 drug discovery

Rohoullah Firouzi, Mitra Ashouri and Mohammad Hossein Karimi‐Jafari

Proteins, 2022, 90, 1090
DOI: 10.1002/prot.26318

Drug repurposing against SARS-CoV-2 using computational approaches

Sumit Kumar, Svitlana Kovalenko, Shakshi Bhardwaj, Aaftaab Sethi, Nikolay Yu. Gorobets, Sergey M. Desenko, Poonam and Brijesh Rathi

Drug Discovery Today, 2022, 27, 2015
DOI: 10.1016/j.drudis.2022.02.004

Utilizing clinical pharmacology in the drug repurposing arena: a look into COVID-19

Rosanna Ruggiero, Nunzia Balzano, Raffaella Di Napoli, Maria Giuseppa Sullo, Francesco Rossi, Annalisa Capuano and Concetta Rafaniello

Expert Review of Clinical Pharmacology, 2022, 15, 1225
DOI: 10.1080/17512433.2022.2132226

A community effort in SARS‐CoV‐2 drug discovery

Johannes Schimunek, Philipp Seidl, Katarina Elez, Tim Hempel, Tuan Le, Frank Noé, Simon Olsson, Lluís Raich, Robin Winter, Hatice Gokcan, Filipp Gusev, Evgeny M. Gutkin, Olexandr Isayev, Maria G. Kurnikova, Chamali H. Narangoda, Roman Zubatyuk, Ivan P. Bosko, Konstantin V. Furs, Anna D. Karpenko, Yury V. Kornoushenko, Mikita Shuldau, Artsemi Yushkevich, Mohammed B. Benabderrahmane, Patrick Bousquet‐Melou, Ronan Bureau, Beatrice Charton, Bertrand C. Cirou, Gérard Gil, William J. Allen, Suman Sirimulla, Stanley Watowich, Nick Antonopoulos, Nikolaos Epitropakis, Agamemnon Krasoulis, Vassilis Pitsikalis, Stavros Theodorakis, Igor Kozlovskii, Anton Maliutin, Alexander Medvedev, Petr Popov, Mark Zaretckii, Hamid Eghbal‐Zadeh, Christina Halmich, Sepp Hochreiter, Andreas Mayr, Peter Ruch, Michael Widrich, Francois Berenger, Ashutosh Kumar, Yoshihiro Yamanishi, Kam Y. J. Zhang, Emmanuel Bengio, Yoshua Bengio, Moksh J. Jain, Maksym Korablyov, Cheng‐Hao Liu, Gilles Marcou, Enrico Glaab, Kelly Barnsley, Suhasini M. Iyengar, Mary Jo Ondrechen, V. Joachim Haupt, Florian Kaiser, Michael Schroeder, Luisa Pugliese, Simone Albani, Christina Athanasiou, Andrea Beccari, Paolo Carloni, Giulia D'Arrigo, Eleonora Gianquinto, Jonas Goßen, Anton Hanke, Benjamin P. Joseph, Daria B. Kokh, Sandra Kovachka, Candida Manelfi, Goutam Mukherjee, Abraham Muñiz‐Chicharro, Francesco Musiani, Ariane Nunes‐Alves, Giulia Paiardi, Giulia Rossetti, S. Kashif Sadiq, Francesca Spyrakis, Carmine Talarico, Alexandros Tsengenes, Rebecca C. Wade, Conner Copeland, Jeremiah Gaiser, Daniel R. Olson, Amitava Roy, Vishwesh Venkatraman, Travis J. Wheeler, Haribabu Arthanari, Klara Blaschitz, Marco Cespugli, Vedat Durmaz, Konstantin Fackeldey, Patrick D. Fischer, Christoph Gorgulla, Christian Gruber, Karl Gruber, Michael Hetmann, Jamie E. Kinney, Krishna M. Padmanabha Das, Shreya Pandita, Amit Singh, Georg Steinkellner, Guilhem Tesseyre, Gerhard Wagner, Zi‐Fu Wang, Ryan J. Yust, Dmitry S. Druzhilovskiy, Dmitry A. Filimonov, Pavel V. Pogodin, Vladimir Poroikov, Anastassia V. Rudik, Leonid A. Stolbov, Alexander V. Veselovsky, Maria De Rosa, Giada De Simone, Maria R. Gulotta, Jessica Lombino, Nedra Mekni, Ugo Perricone, Arturo Casini, Amanda Embree, D. Benjamin Gordon, David Lei, Katelin Pratt, Christopher A. Voigt, Kuang‐Yu Chen, Yves Jacob, Tim Krischuns, Pierre Lafaye, Agnès Zettor, M. Luis Rodríguez, Kris M. White, Daren Fearon, Frank Von Delft, Martin A. Walsh, Dragos Horvath, Charles L. Brooks, Babak Falsafi, Bryan Ford, Adolfo García‐Sastre, Sang Yup Lee, Nadia Naffakh, Alexandre Varnek, Günter Klambauer and Thomas M. Hermans

Molecular Informatics, 2024, 43
DOI: 10.1002/minf.202300262

Chemical transformer compression for accelerating both training and inference of molecular modeling

Yi Yu and Karl Börjesson

Mach. Learn.: Sci. Technol., 2022, 3, 045009
DOI: 10.1088/2632-2153/ac99ba

Identification of SARS-CoV-2 Main Protease Inhibitors Using Chemical Similarity Analysis Combined with Machine Learning

Karina Eurídice Juárez-Mercado, Milton Abraham Gómez-Hernández, Juana Salinas-Trujano, Luis Córdova-Bahena, Clara Espitia, Sonia Mayra Pérez-Tapia, José L. Medina-Franco and Marco A. Velasco-Velázquez

Pharmaceuticals, 2024, 17, 240
DOI: 10.3390/ph17020240

Indirect-Acting Pan-Antivirals vs. Respiratory Viruses: A Fresh Perspective on Computational Multi-Target Drug Discovery

Valeria V. Kleandrova, Marcus T. Scotti and Alejandro Speck-Planche

CTMC, 2021, 21, 2687
DOI: 10.2174/1568026621666211012110819

Phytomedical compounds as promising therapeutic agents for COVID-19 targeting angiotensin-converting enzyme 2: a review

Smail Amtaghri, Miloudia Slaoui and Mohamed Eddouks

Journal of Pharmacy and Pharmacology, 2024, 76, 1239
DOI: 10.1093/jpp/rgae101

Preventive and control system for the life cycle of a pandemic

Chenyang Wang, Rui Ba, Ranpeng Wang and Hui Zhang

Journal of Safety Science and Resilience, 2022, 3, 321
DOI: 10.1016/j.jnlssr.2022.06.002

A review on computational approaches that support the researches on traditional Chinese medicines (TCM) against COVID-19

Chattarin Ruchawapol, Wen-Wei Fu and Hong-Xi Xu

Phytomedicine, 2022, 104, 154324
DOI: 10.1016/j.phymed.2022.154324

COVID-19 infection and neurodegeneration: Computational evidence for interactions between the SARS-CoV-2 spike protein and monoamine oxidase enzymes

Lucija Hok, Hrvoje Rimac, Janez Mavri and Robert Vianello

Computational and Structural Biotechnology Journal, 2022, 20, 1254
DOI: 10.1016/j.csbj.2022.02.020

Structure-based pharmacophore modeling, virtual screening, and molecular dynamics simulation studies for identification of Plasmodium falciparum 5-aminolevulinate synthase inhibitors

Gbolahan O. Oduselu, Rufus Afolabi, Ibitayo Ademuwagun, Ashley Vaughan and Ezekiel Adebiyi

Front. Med., 2023, 9
DOI: 10.3389/fmed.2022.1022429

In Silico Development of SARS-CoV-2 Non-Covalent Mpro Inhibitors: A Review

Islam Alagawani and Feng Wang

Applied Sciences, 2025, 15, 6544
DOI: 10.3390/app15126544

Computational identification of Vernonia cinerea-derived phytochemicals as potential inhibitors of nonstructural protein 1 (NSP1) in dengue virus serotype-2

Md. Shohel Hossain, Soharth Hasnat, Shilpy Akter, Maria Mulla Mim, Anika Tahcin, Majedul Hoque, Durjoy Sutradhar, Mst. Alifa Akter Keya, Namin Rouf Sium, Sophia Hossain, Runa Masuma, Sakhawat Hossen Rakib, Md. Aminul Islam, Tofazzal Islam, Prosun Bhattacharya and M. Nazmul Hoque

Front. Pharmacol., 2024, 15
DOI: 10.3389/fphar.2024.1465827

Prediction of the small molecule selectivity index against influenza virus strain A/H1N1 using machine learning methods

A. D. Egorov, Ya. V. Gorohov, M. M. Kuznetsov and S. S. Borisevich

Russ Chem Bull, 2025, 74, 851
DOI: 10.1007/s11172-025-4579-5

Highly potent dual-targeting angiotensin-converting enzyme 2 (ACE2) and Neuropilin-1 (NRP1) peptides: A promising broad-spectrum therapeutic strategy against SARS-CoV-2 infection

Shuang Mei, Yunting Zou, Su Jiang, Lu Xue, Yuting Wang, Han Jing, Peng Yang, Miao-Miao Niu, Jindong Li, Kai Yuan and Yan Zhang

European Journal of Medicinal Chemistry, 2024, 263, 115908
DOI: 10.1016/j.ejmech.2023.115908

Neoechinulin A as a Promising SARS-CoV-2 Mpro Inhibitor: In Vitro and In Silico Study Showing the Ability of Simulations in Discerning Active from Inactive Enzyme Inhibitors

Hani A. Alhadrami, Gaia Burgio, Bathini Thissera, Raha Orfali, Suzan E. Jiffri, Mohammed Yaseen, Ahmed M. Sayed and Mostafa E. Rateb

Marine Drugs, 2022, 20, 163
DOI: 10.3390/md20030163

Beta-blokerlerin yeniden konumlandırılması: Meme kanseri uygulamaları

Gökçe Nur ÇİTLER and Özlem DARCANSOY İSERİ

Frontiers in Life Sciences and Related Technologies, 2023, 4, 52
DOI: 10.51753/flsrt.1152416

A review on computer‐aided chemogenomics and drug repositioning for rationalCOVID‐19 drug discovery

Saeid Maghsoudi, Bahareh Taghavi Shahraki, Fatemeh Rameh, Masoomeh Nazarabi, Yousef Fatahi, Omid Akhavan, Mohammad Rabiee, Ebrahim Mostafavi, Eder C. Lima, Mohammad Reza Saeb and Navid Rabiee

Chem Biol Drug Des, 2022, 100, 699
DOI: 10.1111/cbdd.14136

Towards a Unified Pandemic Management Architecture: Survey, Challenges, and Future Directions

Satyaki Roy, Nirnay Ghosh, Nitish Uplavikar and Preetam Ghosh

ACM Comput. Surv., 2024, 56, 1
DOI: 10.1145/3609324

What are the current challenges for machine learning in drug discovery and repurposing?

Tero Aittokallio

Expert Opinion on Drug Discovery, 2022, 17, 423
DOI: 10.1080/17460441.2022.2050694

SMILES-based 2D-QSAR and similarity search for identification of potential new scaffolds for development of SARS-CoV-2 MPRO inhibitors

Adriana Santos Costa, João Paulo Ataide Martins and Eduardo Borges de Melo

Struct Chem, 2022, 33, 1691
DOI: 10.1007/s11224-022-02008-9

Identification of potent antimicrobial peptides via a machine-learning pipeline that mines the entire space of peptide sequences

Junjie Huang, Yanchao Xu, Yunfan Xue, Yue Huang, Xu Li, Xiaohui Chen, Yao Xu, Dongxiang Zhang, Peng Zhang, Junbo Zhao and Jian Ji

Nat. Biomed. Eng, 2023, 7, 797
DOI: 10.1038/s41551-022-00991-2

Tackling SARS‐CoV‐2: Deep Purpose Virtual Screening Identified Compounds to Target the Glycosylated Full‐Length GRP78

Wael M. Elshemey, Ibrahim M. Ibrahim, Ahmed A. Ezat, Alaa M. Elgohary, Abdo A. Elfiky and Aaya M. Nassar

Advcd Theory and Sims, 2024, 7
DOI: 10.1002/adts.202400378

Molecular Basis of SARS-CoV-2 Nsp1-Induced Immune Translational Shutdown as Revealed by All-Atom Simulations

Jure Borišek, Angelo Spinello and Alessandra Magistrato

J. Phys. Chem. Lett., 2021, 12, 11745
DOI: 10.1021/acs.jpclett.1c03441

An unprecedented global challenge, emerging trends and innovations in the fight against COVID-19: A comprehensive review

S. Moneshwaran, D. Macrin and N. Kanagathara

International Journal of Biological Macromolecules, 2024, 267, 131324
DOI: 10.1016/j.ijbiomac.2024.131324

Ensemble docking based virtual screening of SARS‐CoV‐2 main protease inhibitors

Anastasia D. Fomina, Victoria I. Uvarova, Liubov I. Kozlovskaya, Vladimir A. Palyulin, Dmitry I. Osolodkin and Aydar A. Ishmukhametov

Molecular Informatics, 2024, 43
DOI: 10.1002/minf.202300279

Exploring innovative strategies for identifying anti-breast cancer compounds by integrating 2D/3D-QSAR, molecular docking analyses, ADMET predictions, molecular dynamics simulations, and MM-PBSA approaches

Said El Rhabori, Marwa Alaqarbeh, Yassine El Allouche, Lhoucine Naanaai, Abdellah El Aissouq, Mohammed Bouachrine, Samir Chtita and Fouad Khalil

Journal of Molecular Structure, 2025, 1320, 139500
DOI: 10.1016/j.molstruc.2024.139500

Autoencoder-based drug-virus association prediction with reliable negative sample selection: A case study with COVID-19

A.S. Aruna, K.R. Remesh Babu and K. Deepthi

Biophysical Chemistry, 2025, 322, 107434
DOI: 10.1016/j.bpc.2025.107434

TwoFold: Highly accurate structure and affinity prediction for protein-ligand complexes from sequences

Darren J Hsu, Hao Lu, Aditya Kashi, Michael Matheson, John Gounley, Feiyi Wang, Wayne Joubert and Jens Glaser

The International Journal of High Performance Computing Applications, 2023, 37, 666
DOI: 10.1177/10943420231201151

CBPDdb: a curated database of compounds derived from Coumarin–Benzothiazole–Pyrazole

Shailima Rampogu, Mohammed Rafi Shaik, Merajuddin Khan, Mujeeb Khan, Tae Hwan Oh and Baji Shaik

Database, 2023, 2023
DOI: 10.1093/database/baad062

Button-Push On-Demand Synthesis for Rapid Optimization of Antiviral Peptidomimetics

Duanshuai Tian, Ting Wei Tan, Ronald Toh Kuan Hai, Gan Wang, Fadhil Peer Mohamed, Zhenyang Yu, Hwee Ting Ang, Weijun Xu, Qian Wen Tan, Pearly Shuyi Ng, Choon Heng Low, Boping Liu, Perlyn Quek Zekui, Joma Kanikadu Joy, Joseph Cherian, Frankie S Mak and Jie Wu

J. Am. Chem. Soc., 2024, 146, 31321
DOI: 10.1021/jacs.4c12834

In-vitro and in-silico evaluation of rue herb for SARS-CoV-2 treatment

Maliha Khandoker Minu, Md Enamul Kabir Talukder, Ramzi A. Mothana, Sk Injamamul Islam, Abdullah R. Alanzi, Sidgi Hasson, Md Irfan Sadique, Mohammed Arfat Raihan Chowdhury, Md Shajid Khan, Foysal Ahammad and Farhan Mohammad

International Immunopharmacology, 2024, 143, 113318
DOI: 10.1016/j.intimp.2024.113318

Nonthermal Biocompatible Plasma Inactivation of Coronavirus SARS-CoV-2: Prospects for Future Antiviral Applications

Ihn Han, Sohail Mumtaz and Eun Ha Choi

Viruses, 2022, 14, 2685
DOI: 10.3390/v14122685

In silico tuning of binding selectivity for new SARS-CoV-2 main protease inhibitors

Feng Wang and Vladislav Vasilyev

Computer Methods and Programs in Biomedicine, 2025, 262, 108678
DOI: 10.1016/j.cmpb.2025.108678

Aloin A inhibits SARS CoV-2 replication by targeting its binding with ACE2 - Evidence from modeling-supported molecular dynamics simulation

Hani A. Alhadrami, Ahmed M. Sayed, Hossam M. Hassan and Mostafa E. Rateb

Journal of Biomolecular Structure and Dynamics, 2023, 41, 11647
DOI: 10.1080/07391102.2023.2175262

Revolutionizing Vaccine Development for COVID-19: A Review of AI-Based Approaches

Aritra Ghosh, Maria M. Larrondo-Petrie and Mirjana Pavlovic

Information, 2023, 14, 665
DOI: 10.3390/info14120665

HyperPCM: Robust Task-Conditioned Modeling of Drug–Target Interactions

Emma Svensson, Pieter-Jan Hoedt, Sepp Hochreiter and Günter Klambauer

J. Chem. Inf. Model., 2024, 64, 2539
DOI: 10.1021/acs.jcim.3c01417

Artificial intelligence–enabled virtual screening of ultra-large chemical libraries with deep docking

Francesco Gentile, Jean Charle Yaacoub, James Gleave, Michael Fernandez, Anh-Tien Ton, Fuqiang Ban, Abraham Stern and Artem Cherkasov

Nat Protoc, 2022, 17, 672
DOI: 10.1038/s41596-021-00659-2

Green and efficient one-pot three-component synthesis of novel drug-like furo[2,3-d]pyrimidines as potential active site inhibitors and putative allosteric hotspots modulators of both SARS-CoV-2 MPro and PLPro

Hossein Mousavi, Behzad Zeynizadeh and Mehdi Rimaz

Bioorganic Chemistry, 2023, 135, 106390
DOI: 10.1016/j.bioorg.2023.106390

RETRACTED: Artemisia Extracts and Artemisinin-Based Antimalarials for COVID-19 Management: Could These Be Effective Antivirals for COVID-19 Treatment?

Pawan Agrawal, Chandan Agrawal and Gerald Blunden

Molecules, 2022, 27, 3828
DOI: 10.3390/molecules27123828

A computational predicting of possible inhibitors of the main SARS-CoV-2 protease found in Algerian herbal medicines

Benalia Yabrir, Assia Belhassan, Guillermo SalgadoMoran, Tahar Lakhlifi, Mohammed Bouachrine and Lorena Gerli Candia

Rev. Colomb. Quim., 2023, 51
DOI: 10.15446/rev.colomb.quim.v51n3.106949

Designing and developing a sensitive and specific SARS-CoV-2 RBD IgG detection kit for identifying positive human samples

Ehsan Raoufi, Fatemeh Hosseini, Bahman Onagh, Mohammad Salehi-Shadkami, Marjan Mehrali, Monireh Mohsenzadegan, Jim Q. Ho, Banafsheh Bigdelou, Mohammad Reza Sepand, Thomas J. Webster, Steven Zanganeh and Mohammad M. Farajollahi

Clinica Chimica Acta, 2023, 542, 117279
DOI: 10.1016/j.cca.2023.117279

Repurposing the antibacterial drugs for inhibition of SARS-CoV2-PLpro using molecular docking, MD simulation and binding energy calculation

Rohit Patel, Jignesh Prajapati, Priyashi Rao, Rakesh M. Rawal, Meenu Saraf and Dweipayan Goswami

Mol Divers, 2022, 26, 2189
DOI: 10.1007/s11030-021-10325-0

Defending Antiviral Cationic Amphiphilic Drugs That May Cause Drug-Induced Phospholipidosis

Thomas R. Lane and Sean Ekins

J. Chem. Inf. Model., 2021, 61, 4125
DOI: 10.1021/acs.jcim.1c00903

Molecular Docking and ADME-TOX Profiling of Moringa oleifera Constituents against SARS-CoV-2

Hellen Cris Araújo Souza, Maycon Douglas Araújo Souza, Cássio Silva Sousa, Edilanne Katrine Amparo Viana, Sabrina Kelly Silva Alves, Alex Oliveira Marques, Arthur Serejo Neves Ribeiro, Vanessa de Sousa do Vale, Muhammad Torequl Islam, João Antônio Leal de Miranda, Marcelo da Costa Mota and Jefferson Almeida Rocha

ARM, 2023, 91, 464
DOI: 10.3390/arm91060035

Mechanistic Insights into Targeting SARS-CoV-2 Papain-like Protease in the Evolution and Management of COVID-19

Nonjabulo Ntombikhona Magwaza, Aganze Gloire-Aimé Mushebenge, Samuel Chima Ugbaja, Nonkululeko Avril Mbatha, Rene B. Khan and Hezekiel M. Kumalo

BioChem, 2024, 4, 268
DOI: 10.3390/biochem4030014

In Silico Therapeutic Study: The Next Frontier in the Fight against SARS-CoV-2 and Its Variants

Calvin R. Wei, Zarrin Basharat and Godwin C. Lang’at

DDC, 2024, 3, 54
DOI: 10.3390/ddc3010005

Pyronaridine Protects against SARS-CoV-2 Infection in Mouse

Ana C. Puhl, Giovanni F. Gomes, Samara Damasceno, Andre S. Godoy, Gabriela D. Noske, Aline M. Nakamura, Victor O. Gawriljuk, Rafaela S. Fernandes, Natalia Monakhova, Olga Riabova, Thomas R. Lane, Vadim Makarov, Flavio P. Veras, Sabrina S. Batah, Alexandre T. Fabro, Glaucius Oliva, Fernando Q. Cunha, José C. Alves-Filho, Thiago M. Cunha and Sean Ekins

ACS Infect. Dis., 2022, 8, 1147
DOI: 10.1021/acsinfecdis.2c00091

Machine learning in preclinical drug discovery

Denise B. Catacutan, Jeremie Alexander, Autumn Arnold and Jonathan M. Stokes

Nat Chem Biol, 2024, 20, 960
DOI: 10.1038/s41589-024-01679-1

SARS-CoV-2 replication and drug discovery

Farah Nazir, Arnaud John Kombe Kombe, Zunera Khalid, Shaheen Bibi, Hongliang Zhang, Songquan Wu and Tengchuan Jin

Molecular and Cellular Probes, 2024, 77, 101973
DOI: 10.1016/j.mcp.2024.101973

Structural, Electronic, Reactivity, and Conformational Features of 2,5,5-Trimethyl-1,3,2-diheterophosphinane-2-sulfide, and Its Derivatives: DFT, MEP, and NBO Calculations

Nasrin Masnabadi, Mohammad R. Thalji, Huda S. Alhasan, Zahra Mahmoodi, Alexander V. Soldatov and Gomaa A. M. Ali

Molecules, 2022, 27, 4011
DOI: 10.3390/molecules27134011

Computational and artificial intelligence-based methods for antibody development

Jisun Kim, Matthew McFee, Qiao Fang, Osama Abdin and Philip M. Kim

Trends in Pharmacological Sciences, 2023, 44, 175
DOI: 10.1016/j.tips.2022.12.005

Computational approaches for modeling and structural design of biological systems: A comprehensive review

Ekambaram Gayathiri, Palanisamy Prakash, Priya Kumaravel, Jayanthi Jayaprakash, Manikkavalli Gurunathan Ragunathan, Sharmila Sankar, Saravanan Pandiaraj, Natesan Thirumalaivasan, Muthu Thiruvengadam and Rajakumar Govindasamy

Progress in Biophysics and Molecular Biology, 2023, 185, 17
DOI: 10.1016/j.pbiomolbio.2023.08.002

Computational repurposing of drugs for viral diseases and current and future pandemics

David A. Winkler

J Math Chem, 2024, 62, 2844
DOI: 10.1007/s10910-023-01568-3

An Overview of SARS-CoV-2 Potential Targets, Inhibitors, and Computational Insights to Enrich the Promising Treatment Strategies

Pooja Kumawat, Lokesh Kumar Agarwal and Kuldeep Sharma

Curr Microbiol, 2024, 81
DOI: 10.1007/s00284-024-03671-3

Protein–ligand interactions from a quantum fragmentation perspective: The case of the SARS-CoV-2 main protease interacting with α-ketoamide inhibitors

Luigi Genovese, William Dawson, Takahito Nakajima, Viviana Cristiglio, Valérie Vallet and Michel Masella

The Journal of Chemical Physics, 2023, 158
DOI: 10.1063/5.0148064

Structure-Based In Silico Screening of Marine Phlorotannins for Potential Walrus Calicivirus Inhibitor

Nalae Kang, Eun-A Kim, Seong-Yeong Heo and Soo-Jin Heo

IJMS, 2023, 24, 15774
DOI: 10.3390/ijms242115774

Allosteric Binders of ACE2 Are Promising Anti-SARS-CoV-2 Agents

Joshua E. Hochuli, Sankalp Jain, Cleber Melo-Filho, Zoe L. Sessions, Tesia Bobrowski, Jun Choe, Johnny Zheng, Richard Eastman, Daniel C. Talley, Ganesha Rai, Anton Simeonov, Alexander Tropsha, Eugene N. Muratov, Bolormaa Baljinnyam and Alexey V. Zakharov

ACS Pharmacol. Transl. Sci., 2022, 5, 468
DOI: 10.1021/acsptsci.2c00049

From De Novo Design to Redesign: Harnessing Computational Protein Design for Understanding SARS-CoV-2 Molecular Mechanisms and Developing Therapeutics

Aditya K. Padhi, Parismita Kalita, Shweata Maurya, Krishna Mohan Poluri and Timir Tripathi

J. Phys. Chem. B, 2023, 127, 8717
DOI: 10.1021/acs.jpcb.3c04542

The Potential of Anti-coronavirus Plant Secondary Metabolites in COVID-19 Drug Discovery as an Alternative to Repurposed Drugs: A Review

Zahra Alipour, Somayeh Zarezadeh and Ali Akbar Ghotbi-Ravandi

Planta Med, 2024, 90, 172
DOI: 10.1055/a-2209-6357

A Review of Computational Approaches Targeting SARS-CoV-2 Main Protease to the Discovery of New Potential Antiviral Compounds

Juan A. Castillo-Garit, Yudith Cañizares-Carmenate, Hai Pham-The, Virginia Pérez-Doñate, Francisco Torrens and Facundo Pérez-Giménez

CTMC, 2023, 23, 3
DOI: 10.2174/2667387816666220426133555

DINC-COVID: A webserver for ensemble docking with flexible SARS-CoV-2 proteins

Sarah Hall-Swan, Didier Devaurs, Mauricio M. Rigo, Dinler A. Antunes, Lydia E. Kavraki and Geancarlo Zanatta

Computers in Biology and Medicine, 2021, 139, 104943
DOI: 10.1016/j.compbiomed.2021.104943

How can artificial intelligence be utilized for de novo drug design against COVID-19 (SARS-CoV-2)?

Giuseppe Floresta, Chiara Zagni, Vincenzo Patamia and Antonio Rescifina

Expert Opinion on Drug Discovery, 2023, 18, 1061
DOI: 10.1080/17460441.2023.2236930

Exploring Cannabinoids as Potential Inhibitors of SARS-CoV-2 Papain-like Protease: Insights from Computational Analysis and Molecular Dynamics Simulations

Jamie Holmes, Shahidul M. Islam and Kimberly A. Milligan

Viruses, 2024, 16, 878
DOI: 10.3390/v16060878

Computational Protein Design for COVID-19 Research and Emerging Therapeutics

Parismita Kalita, Timir Tripathi and Aditya K. Padhi

ACS Cent. Sci., 2023, 9, 602
DOI: 10.1021/acscentsci.2c01513

Natural Products for the Prevention and Control of the COVID-19 Pandemic: Sustainable Bioresources

Rajeev K. Singla, Xuefei He, Hitesh Chopra, Christos Tsagkaris, Li Shen, Mohammad Amjad Kamal and Bairong Shen

Front. Pharmacol., 2021, 12
DOI: 10.3389/fphar.2021.758159

Machine Learning Models Identify Inhibitors of SARS-CoV-2

Victor O. Gawriljuk, Phyo Phyo Kyaw Zin, Ana C. Puhl, Kimberley M. Zorn, Daniel H. Foil, Thomas R. Lane, Brett Hurst, Tatyana Almeida Tavella, Fabio Trindade Maranhão Costa, Premkumar Lakshmanane, Jean Bernatchez, Andre S. Godoy, Glaucius Oliva, Jair L. Siqueira-Neto, Peter B. Madrid and Sean Ekins

J. Chem. Inf. Model., 2021, 61, 4224
DOI: 10.1021/acs.jcim.1c00683

Identification of Potential Anti‐COVID‐19 Drug Leads from Medicinal Plants through Virtual High‐Throughput Screening

Rohoullah Firouzi and Mitra Ashouri

ChemistrySelect, 2023, 8
DOI: 10.1002/slct.202203865

Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2

Kaifu Gao, Rui Wang, Jiahui Chen, Limei Cheng, Jaclyn Frishcosy, Yuta Huzumi, Yuchi Qiu, Tom Schluckbier, Xiaoqi Wei and Guo-Wei Wei

Chem. Rev., 2022, 122, 11287
DOI: 10.1021/acs.chemrev.1c00965

A Review on Artificial Intelligence Approaches and Rational Approaches in Drug Discovery

Anjana Vidya Srivathsa, Nandini Markuli Sadashivappa, Apeksha Krishnamurthy Hegde, Srimathi Radha, Agasa Ramu Mahesh, Damodar Nayak Ammunje, Debanjan Sen, Panneerselvam Theivendren, Saravanan Govindaraj, Selvaraj Kunjiappan and Parasuraman Pavadai

CPD, 2023, 29, 1180
DOI: 10.2174/1381612829666230428110542

Discovery of raffinose sulfate as a potential SARS CoV-2 inhibitor via blocking its binding with angiotensin converting enzyme 2

Rami Adel Pashameah, Raya Soltane and Ahmed M. Sayed

International Journal of Biological Macromolecules, 2023, 248, 125818
DOI: 10.1016/j.ijbiomac.2023.125818

Artificial Intelligence for Drug Discovery: Are We There Yet?

Catrin Hasselgren and Tudor I. Oprea

Annu. Rev. Pharmacol. Toxicol., 2024, 64, 527
DOI: 10.1146/annurev-pharmtox-040323-040828

Effect of an Inhibitor on the ACE2-Receptor-Binding Domain of SARS-CoV-2

Gaurav Sharma, Lin Frank Song and Kenneth M. Merz

J. Chem. Inf. Model., 2022, 62, 6574
DOI: 10.1021/acs.jcim.1c01283

Identification of Potential Ligands of the Main Protease of Coronavirus SARS-CoV-2 (2019-nCoV) Using Multimodal Generative Neural-Networks

Syeda Rehana Zia

Fr. Ukr. J. Chem., 2022, 10, 30
DOI: 10.17721/fujcV10I1P30-47

DRUG REPOSITIONING FOR THERAPY OF COVID-19

V.V. Poroikov, D.S. Druzhilovskiy, P.I. Savosina, O.A. Gomazkov, B.N. Sobolev, A.V. Veselovsky, O.A. Tarasova, N.Yu. Biziukova, N.S. Ionov, S.M. Ivanov, A.V Rudik, L.A. Stolbov, P.V. Pogodin, D.A. Karasev, D.A. Dmitriev, A.A. Lagunin and D.A. Filimonov

BIOTECHNOLOGY: STATE OF THE ART AND PERSPECTIVES, 2021, 1, 209
DOI: 10.37747/2312-640X-2021-19-209-211

Impact of Warhead Modulations on the Covalent Inhibition of SARS-CoV-2 Mpro Explored by QM/MM Simulations

Sergio Martí, Kemel Arafet, Alessio Lodola, Adrian J. Mulholland, Katarzyna Świderek and Vicent Moliner

ACS Catal., 2022, 12, 698
DOI: 10.1021/acscatal.1c04661

Identification of a broad-spectrum high-affinity peptide ligand for the purification of spike proteins

Mengke Hu, Xiaoyan Dong, Qinghong Shi and Yan Sun

Journal of Chromatography A, 2024, 1723, 464912
DOI: 10.1016/j.chroma.2024.464912

In Silico Identification of Potential Inhibitors of SARS-CoV-2 Main Protease (Mpro)

Manuel Alejandro Hernández-Serda, Víctor H. Vázquez-Valadez, Pablo Aguirre-Vidal, Nathan M. Markarian, José L. Medina-Franco, Luis Alfonso Cardenas-Granados, Aldo Yoshio Alarcón-López, Pablo A. Martínez-Soriano, Ana María Velázquez-Sánchez, Rodolfo E. Falfán-Valencia, Enrique Angeles and Levon Abrahamyan

Pathogens, 2024, 13, 887
DOI: 10.3390/pathogens13100887

Computational design of stapled peptide inhibitor against SARS‐CoV‐2 receptor binding domain

Asha Rani Choudhury, Atanu Maity, Sayantani Chakraborty and Rajarshi Chakrabarti

Peptide Science, 2022, 114
DOI: 10.1002/pep2.24267

Unravelling viral dynamics through molecular dynamics simulations - A brief overview

Subhomoi Borkotoky, Debajit Dey, Zaved Hazarika, Amit Joshi and Keshawanand Tripathi

Biophysical Chemistry, 2022, 291, 106908
DOI: 10.1016/j.bpc.2022.106908

Discovery of PLpro and Mpro Inhibitors for SARS-CoV-2

Ana C. Puhl, Andre S. Godoy, Gabriela D. Noske, Aline M. Nakamura, Victor O. Gawriljuk, Rafaela S. Fernandes, Glaucius Oliva and Sean Ekins

ACS Omega, 2023, 8, 22603
DOI: 10.1021/acsomega.3c01110

Learning from COVID-19: How drug hunters can prepare for the next pandemic

Ana C. Puhl, Thomas R. Lane and Sean Ekins

Drug Discovery Today, 2023, 28, 103723
DOI: 10.1016/j.drudis.2023.103723

Computational Screening of Plant-Derived Natural Products against SARS-CoV-2 Variants

Waseem Ahmad Ansari, Mohd Aamish Khan, Fahmina Rizvi, Kajim Ali, Mohd Kamil Hussain, Mohammad Saquib and Mohammad Faheem Khan

Future Pharmacology, 2022, 2, 558
DOI: 10.3390/futurepharmacol2040034

Identification of antiviral phytochemicals as a potential SARS-CoV-2 main protease (Mpro) inhibitor using docking and molecular dynamics simulations

Chirag N. Patel, Siddhi P. Jani, Dharmesh G. Jaiswal, Sivakumar Prasanth Kumar, Naman Mangukia, Robin M. Parmar, Rakesh M. Rawal and Himanshu A. Pandya

Sci Rep, 2021, 11
DOI: 10.1038/s41598-021-99165-4

In Silico Modeling as a Perspective in Developing Potential Vaccine Candidates and Therapeutics for COVID-19

Reham F. Barghash, Iten M. Fawzy, Vaisali Chandrasekar, Ajay Vikram Singh, Uma Katha and Asmaa A. Mandour

Coatings, 2021, 11, 1273
DOI: 10.3390/coatings11111273

Taming the cytokine storm: small molecule inhibitors targeting IL-6/IL-6α receptor

Komal Zia, Mohammad Nur-e-Alam, Aftab Ahmad and Zaheer Ul-Haq

Mol Divers, 2024, 28, 4151
DOI: 10.1007/s11030-023-10805-5

Drug repositioning as a promising approach for the eradication of emerging and re-emerging viral agents

Marwa Almulhim, Abdolmajid Ghasemian, Mojtaba Memariani, Farnaz Karami, Asmaa S. A. Yassen, Athanasios Alexiou, Marios Papadakis and Gaber El-Saber Batiha

Mol Divers, 2025
DOI: 10.1007/s11030-025-11131-8

Exploring the molecular potential of natural products against COVID-19 through molecular modeling and machine learning

Rafael Vieira, Vitor Hugo Batista and Kally Alves de Sousa

Next Research, 2025, 2, 100511
DOI: 10.1016/j.nexres.2025.100511

The Need for Speed and Efficiency: A Brief Review of Small Molecule Antivirals for COVID-19

Ana C. Puhl, Thomas R. Lane, Fabio Urbina and Sean Ekins

Front. Drug. Discov., 2022, 2
DOI: 10.3389/fddsv.2022.837587

The Chameleon Strategy—A Recipe for Effective Ligand Screening for Viral Targets Based on Four Novel Structure–Binding Strength Indices

Magdalena Latosińska and Jolanta Natalia Latosińska

Viruses, 2024, 16, 1073
DOI: 10.3390/v16071073

In‐Silico Screening, Molecular Dynamics, and DFT Analysis of ZINC and ChEMBL Library Compounds for SARS‐CoV‐2 Main Protease Inhibition

Soumya Verma, Amit Dubey, Rashika Singh, Rajratna Tayade and Vipin Kumar Mishra

ChemistrySelect, 2025, 10
DOI: 10.1002/slct.202403269

Identification of potential antiviral lead inhibitors against SARS-CoV-2 main protease: Structure-guided virtual screening, docking, ADME, and MD Simulation based approach

Goverdhan Lanka, Revanth Bathula, Balaram Ghosh and Sarita Rajender Potlapally

Artificial Intelligence Chemistry, 2023, 1, 100015
DOI: 10.1016/j.aichem.2023.100015

Intelligent resolution: Integrating Cryo-EM with AI-driven multi-resolution simulations to observe the severe acute respiratory syndrome coronavirus-2 replication-transcription machinery in action

Anda Trifan, Defne Gorgun, Michael Salim, Zongyi Li, Alexander Brace, Maxim Zvyagin, Heng Ma, Austin Clyde, David Clark, David J Hardy, Tom Burnley, Lei Huang, John McCalpin, Murali Emani, Hyenseung Yoo, Junqi Yin, Aristeidis Tsaris, Vishal Subbiah, Tanveer Raza, Jessica Liu, Noah Trebesch, Geoffrey Wells, Venkatesh Mysore, Thomas Gibbs, James Phillips, S Chakra Chennubhotla, Ian Foster, Rick Stevens, Anima Anandkumar, Venkatram Vishwanath, John E Stone, Emad Tajkhorshid, Sarah A Harris and Arvind Ramanathan

The International Journal of High Performance Computing Applications, 2022, 36, 603
DOI: 10.1177/10943420221113513

Multi-structural molecular docking (MOD) combined with molecular dynamics reveal the structural requirements of designing broad-spectrum inhibitors of SARS-CoV-2 entry to host cells

Anqi Da, Meritxell Wu-Lu, Jovan Dragelj, Maria Andrea Mroginski and Kourosh H. Ebrahimi

Sci Rep, 2023, 13
DOI: 10.1038/s41598-023-42015-2

Identifying SARS-CoV-2 Drugs Binding to the Spike Fatty Acid Binding Pocket Using In Silico Docking and Molecular Dynamics

Sakshi Piplani, Puneet Singh, Nikolai Petrovsky and David A. Winkler

IJMS, 2023, 24, 4192
DOI: 10.3390/ijms24044192

Theoretical Investigation of the Cooperation of Iminoguanidine with the Enzymes-Binding Domain of Covid-19 and Bacterial Lysozyme Inhibitors and their Pharmacokinetic Properties

Emmanuel Israel Edache, Adamu Uzairu, Paul Andrew Mamza and Gideon Adamu Shallangwa

J. Mex. Chem. Soc., 2022, 66
DOI: 10.29356/jmcs.v66i4.1726

Computational Approaches in the Discovery and Development of Therapeutic and Prophylactic Agents for Viral Diseases

Anand Gaurav, Neetu Agrawal, Mayasah Al-Nema and Vertika Gautam

CTMC, 2022, 22, 2190
DOI: 10.2174/1568026623666221019110334

Investigation of substituent effects on the electronic structure and antiviral activity of favipiravir derivatives for Covid-19 treatment using DFT and molecular docking

Dereje Fedasa Tegegn, Habtamu Zewude Belachew, Habtamu Fekadu Etefa and Ayodeji Olalekan Salau

Sci Rep, 2024, 14
DOI: 10.1038/s41598-024-68712-0

Triterpene Derivatives as Potential Inhibitors of the RBD Spike Protein from SARS-CoV-2: An In Silico Approach

Mayra Avelar, Laura Pedraza-González, Adalgisa Sinicropi and Virginia Flores-Morales

Molecules, 2023, 28, 2333
DOI: 10.3390/molecules28052333

The Six Ds of Exponentials and drug discovery: A path toward reversing Eroom’s law

Alexander Tropsha, Holli-Joi Martin and Artem Cherkasov

Drug Discovery Today, 2025, 30, 104341
DOI: 10.1016/j.drudis.2025.104341

Setomimycin as a potential molecule for COVID‑19 target: in silico approach and in vitro validation

Ravi S. Manhas, Harshita Tiwari, Mateen Noor, Ajaz Ahmed, Jyoti Vishwakarma, Raja B. M. Tripathi, Ravishankar Ramachandran, Sreedhar Madishetti, Debaraj Mukherjee, Amit Nargotra and Asha Chaubey

Mol Divers, 2023, 27, 619
DOI: 10.1007/s11030-022-10441-5

Polyphenolic Natural Products Active In Silico Against SARS-CoV-2 Spike Receptor Binding Domains and Non-structural Proteins - A Review

Mark Tristan Quimque, Kin Israel Notarte, Xela Amor Adviento, Mikhail Harvey Cabunoc, Von Novi de Leon, Felippe Steven Louis delos Reyes, Eiron John Lugtu, Joe Anthony Manzano, Sofia Nicole Monton, John Emmanuel Muñoz, Katherine Denise Ong, Delfin Yñigo Pilapil, Vito Roque, Sophia Morgan Tan, Justin Allen Lim and Allan Patrick Macabeo

CCHTS, 2023, 26, 459
DOI: 10.2174/1386207325666210917113207

Drug repositioning: A bibliometric analysis

Guojun Sun, Dashun Dong, Zuojun Dong, Qian Zhang, Hui Fang, Chaojun Wang, Shaoya Zhang, Shuaijun Wu, Yichen Dong and Yuehua Wan

Front. Pharmacol., 2022, 13
DOI: 10.3389/fphar.2022.974849

Discovery of host-directed modulators of virus infection by probing the SARS-CoV-2–host protein–protein interaction network

Vandana Ravindran, Jessica Wagoner, Paschalis Athanasiadis, Andreas B Den Hartigh, Julia M Sidorova, Aleksandr Ianevski, Susan L Fink, Arnoldo Frigessi, Judith White, Stephen J Polyak and Tero Aittokallio

Briefings in Bioinformatics, 2022, 23
DOI: 10.1093/bib/bbac456

Fragment databases from screened ligands for drug discovery (FDSL-DD)

Jerica Wilson, Bahrad A. Sokhansanj, Wei Chuen Chong, Rohan Chandraghatgi, Gail L. Rosen and Hai-Feng Ji

Journal of Molecular Graphics and Modelling, 2024, 127, 108669
DOI: 10.1016/j.jmgm.2023.108669

Prediction of deleterious non-synonymous SNPs of TMPRSS2 protein combined with Molecular Dynamics Simulations and free energy analysis to identify the potential peptide substrates against SARS-CoV-2

Balajee Ramachandran, Ahmed Nadeem, Aruchamy Mohanprasanth and Muthupandian Saravanan

Journal of Biomolecular Structure and Dynamics, 2024, 1
DOI: 10.1080/07391102.2024.2330710

The diverse role of heparan sulfate and other GAGs in SARS-CoV-2 infections and therapeutics

Friederike Eilts, Sarah Bauer, Keith Fraser, Jonathan S. Dordick, Michael W. Wolff, Robert J. Linhardt and Fuming Zhang

Carbohydrate Polymers, 2023, 299, 120167
DOI: 10.1016/j.carbpol.2022.120167

Biological exploration of theophylline-appended acetamides as anti-SARS-CoV-2 agents targeting main protease (Mpro), spike glycoprotein and RNA-dependent RNA polymerase (RdRp)

Ramsha Munir, Ameer Fawad Zahoor, Muhammad Jawwad Saif, Freeha Hafeez, Usman Nazeer, Bushra Parveen and Sajjad Ahmad

Journal of Molecular Structure, 2025, 1343, 142858
DOI: 10.1016/j.molstruc.2025.142858

Insights into the Interaction Mechanism of Boceprevir with SARS‐CoV‐2 Main Protease

Gurmeet Kaur and Bhupesh Goyal

ChemistrySelect, 2023, 8
DOI: 10.1002/slct.202301415

Unlocking antiviral potentials of traditional plants: A multi-method computational study against human metapneumovirus (HMPV)

Amit Dubey, Manish Kumar, Aisha Tufail, Vivek Dhar Dwivedi and Andrea Ragusa

Journal of Infection and Public Health, 2025, 18, 102885
DOI: 10.1016/j.jiph.2025.102885

GINCM-DTA: A graph isomorphic network with protein contact map representation for potential use against COVID-19 and Omicron subvariants BQ.1, BQ.1.1, XBB.1.5, XBB.1.16

Guanxing Chen, Haohuai He, Lu Zhao, Qiujie Lv and Calvin Yu-Chian Chen

Expert Systems with Applications, 2024, 236, 121274
DOI: 10.1016/j.eswa.2023.121274

Machine learning prediction of 3CL SARS-CoV-2 docking scores

Lukas Bucinsky, Dušan Bortňák, Marián Gall, Ján Matúška, Viktor Milata, Michal Pitoňák, Marek Štekláč, Daniel Végh and Dávid Zajaček

Computational Biology and Chemistry, 2022, 98, 107656
DOI: 10.1016/j.compbiolchem.2022.107656

Comprehensive exploration of thiophene-tagged 2-(2-hydrazinyl)thiazole derivatives: Synthesis, structural characterization, antimicrobial potential, and computational insights

Rahul A. Shinde, Vishnu A. Adole, Gauri S. Bagdane, Bapu S. Jagdale, Ammar A. Razzak Mahmood, Iqrar Ahmad, Harun Patel and Om Prakash

Journal of Molecular Structure, 2025, 1341, 142453
DOI: 10.1016/j.molstruc.2025.142453

The commoditization of AI for molecule design

Fabio Urbina and Sean Ekins

Artificial Intelligence in the Life Sciences, 2022, 2, 100031
DOI: 10.1016/j.ailsci.2022.100031

Interface-Based Design of High-Affinity Affibody Ligands for the Purification of RBD from Spike Proteins

Siyuan Song and Qinghong Shi

Molecules, 2023, 28, 6358
DOI: 10.3390/molecules28176358

Recent advances in drug repurposing using machine learning

Fabio Urbina, Ana C. Puhl and Sean Ekins

Current Opinion in Chemical Biology, 2021, 65, 74
DOI: 10.1016/j.cbpa.2021.06.001

Hybrid In Silico Approach Reveals Novel Inhibitors of Multiple SARS-CoV-2 Variants

Sankalp Jain, Daniel C. Talley, Bolormaa Baljinnyam, Jun Choe, Quinlin Hanson, Wei Zhu, Miao Xu, Catherine Z. Chen, Wei Zheng, Xin Hu, Min Shen, Ganesha Rai, Matthew D. Hall, Anton Simeonov and Alexey V. Zakharov

ACS Pharmacol. Transl. Sci., 2021, 4, 1675
DOI: 10.1021/acsptsci.1c00176

Plant Protease Inhibitors Against SARS-CoV-2 Main Protease: An In⟓ilico Approach

Adrianne M Lima, Adson A de Souza, Jackson L Amaral, Valder N Freire, Pedro F N Souza and Hermógenes D de Oliveira

Future Virol., 2023, 18, 439
DOI: 10.2217/fvl-2022-0189

Machine Learning in the Development of Adsorbents for Clean Energy Application and Greenhouse Gas Capture

Haoxin Mai, Tu C. Le, Dehong Chen, David A. Winkler and Rachel A. Caruso

Advanced Science, 2022, 9
DOI: 10.1002/advs.202203899

An interaction-based drug discovery screen explains known SARS-CoV-2 inhibitors and predicts new compound scaffolds

Philipp Schake, Klevia Dishnica, Florian Kaiser, Christoph Leberecht, V. Joachim Haupt and Michael Schroeder

Sci Rep, 2023, 13
DOI: 10.1038/s41598-023-35671-x

Discriminating High from Low Energy Conformers of Druglike Molecules: An Assessment of Machine Learning Potentials and Quantum Chemical Methods

Linghan Kong and Richard A. Bryce

ChemPhysChem, 2025, 26
DOI: 10.1002/cphc.202400992

Identification and Development of Therapeutics for COVID-19

Halie M. Rando, Nils Wellhausen, Soumita Ghosh, Alexandra J. Lee, Anna Ada Dattoli, Fengling Hu, James Brian Byrd, Diane N. Rafizadeh, Ronan Lordan, Yanjun Qi, Yuchen Sun, Christian Brueffer, Jeffrey M. Field, Marouen Ben Guebila, Nafisa M. Jadavji, Ashwin N. Skelly, Bharath Ramsundar, Jinhui Wang, Rishi Raj Goel, YoSon Park, Simina M. Boca, Anthony Gitter, Casey S. Greene and Jack A. Gilbert

mSystems, 2021, 6
DOI: 10.1128/mSystems.00233-21

High performance-oriented computer aided drug design approaches in the exascale era

Andrea Rizzi and Davide Mandelli

Expert Opinion on Drug Discovery, 2025, 20, 391
DOI: 10.1080/17460441.2025.2468289