Potential inhibitors for SARS-CoV-2 Mpro from marine compounds

Nguyen Minh Tam, Minh Quan Pham, Huy Truong Nguyen, Nam Dao Hong, Nguyen Khoa Hien, Duong Tuan Quang, Huong Thi Thu Phung and Son Tung Ngo

RSC Adv., 2021, 11, 22206
DOI: 10.1039/D1RA03852D

Anti-multiple myeloma potential of resynthesized belinostat derivatives: an experimental study on cytotoxic activity, drug combination, and docking studies

Hong Phuong Nguyen, Quang De Tran, Cuong Quoc Nguyen, Tran Phuong Hoa, Tran Duy Binh, Huynh Nhu Thao, Bui Thi Buu Hue, Nguyen Trong Tuan, Quang Le Dang, Nguyen Quoc Chau Thanh, Nguyen Van Ky, Minh Quan Pham and Su-Geun Yang

RSC Adv., 2022, 12, 22108
DOI: 10.1039/D2RA01969H

Insights into the binding and covalent inhibition mechanism of PF-07321332 to SARS-CoV-2 Mpro

Son Tung Ngo, Trung Hai Nguyen, Nguyen Thanh Tung and Binh Khanh Mai

RSC Adv., 2022, 12, 3729
DOI: 10.1039/D1RA08752E

Characterizing the ligand-binding affinity toward SARS-CoV-2 Mproviaphysics- and knowledge-based approaches

Son Tung Ngo, Trung Hai Nguyen, Nguyen Thanh Tung, Van V. Vu, Minh Quan Pham and Binh Khanh Mai

Phys. Chem. Chem. Phys., 2022, 24, 29266
DOI: 10.1039/D2CP04476E

Computational estimation of potential inhibitors from known drugs against the main protease of SARS-CoV-2

Nguyen Minh Tam, Minh Quan Pham, Nguyen Xuan Ha, Pham Cam Nam and Huong Thi Thu Phung

RSC Adv., 2021, 11, 17478
DOI: 10.1039/D1RA02529E

Assessing potential inhibitors of SARS-CoV-2 main protease from available drugs using free energy perturbation simulations

Son Tung Ngo, Hung Minh Nguyen, Le Thi Thuy Huong, Pham Minh Quan, Vi Khanh Truong, Nguyen Thanh Tung and Van V. Vu

RSC Adv., 2020, 10, 40284
DOI: 10.1039/D0RA07352K

Binding of inhibitors to the monomeric and dimeric SARS-CoV-2 Mpro

Nguyen Minh Tam, Pham Cam Nam, Duong Tuan Quang, Nguyen Thanh Tung, Van V. Vu and Son Tung Ngo

RSC Adv., 2021, 11, 2926
DOI: 10.1039/D0RA09858B

Searching and designing potential inhibitors for SARS-CoV-2 Mpro from natural sources using atomistic and deep-learning calculations

Nguyen Minh Tam, Duc-Hung Pham, Dinh Minh Hiep, Phuong-Thao Tran, Duong Tuan Quang and Son Tung Ngo

RSC Adv., 2021, 11, 38495
DOI: 10.1039/D1RA06534C

Molecular design of anticancer drugs from marine fungi derivatives

Duc Tuan Cao, Thi Mai Huong Doan, Van Cuong Pham, Thi Hong Minh Le, Jung-Woo Chae, Hwi-yeol Yun, Min-Kyun Na, Young-Ho Kim, Minh Quan Pham and Van Hung Nguyen

RSC Adv., 2021, 11, 20173
DOI: 10.1039/D1RA01855H

Structure-Based Virtual Screening and Biochemical Validation to Discover a Potential Inhibitor of the SARS-CoV-2 Main Protease

Akshita Gupta, Chitra Rani, Pradeep Pant, Viswanathan Vijayan, Naval Vikram, Punit Kaur, Tej Pal Singh, Sujata Sharma and Pradeep Sharma

ACS Omega, 2020, 5, 33151
DOI: 10.1021/acsomega.0c04808

501Y.V2 spike protein resists the neutralizing antibody in atomistic simulations

Son Tung Ngo

Computational Biology and Chemistry, 2022, 97, 107636
DOI: 10.1016/j.compbiolchem.2022.107636

Estimating AChE inhibitors from MCE database by machine learning and atomistic calculations

Quynh Mai Thai, Trung Hai Nguyen, George Binh Lenon, Huong Thi Thu Phung, Jim-Tong Horng, Phuong-Thao Tran and Son Tung Ngo

Journal of Molecular Graphics and Modelling, 2025, 134, 108906
DOI: 10.1016/j.jmgm.2024.108906

Unbinding ligands from SARS-CoV-2 Mpro via umbrella sampling simulations

Nguyen Minh Tam, Trung Hai Nguyen, Vu Thi Ngan, Nguyen Thanh Tung and Son Tung Ngo

R. Soc. open sci., 2022, 9
DOI: 10.1098/rsos.211480

Designing Potential Inhibitors of SARS-CoV-2 Mpro Using Deep Learning and Steered Molecular Dynamic Simulations

Nguyen Minh Tam, Linh Hoang Tran, Quan V. Vo, Minh Quan Pham and Huong Thi Thu Phung

J. Comput. Biophys. Chem., 2023, 22, 525
DOI: 10.1142/S2737416523500242

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

Exploration of potential inhibitors for SARS‐CoV‐2 Mpro considering its mutants via structure‐based drug design, molecular docking, MD simulations, MM/PBSA, and DFT calculations

Abdulrahman Ghasemlou, Vuk Uskoković and Yahya Sefidbakht

Biotech and App Biochem, 2023, 70, 439
DOI: 10.1002/bab.2369

Acetylcholinesterase Inhibitory Activities of Essential Oils from Vietnamese Traditional Medicinal Plants

Nguyen Huy Hung, Pham Minh Quan, Prabodh Satyal, Do Ngoc Dai, Vo Van Hoa, Ngo Gia Huy, Le Duc Giang, Nguyen Thi Ha, Le Thi Huong, Vu Thi Hien and William N. Setzer

Molecules, 2022, 27, 7092
DOI: 10.3390/molecules27207092

Benchmarking the Ability of Common Docking Programs to Correctly Reproduce and Score Binding Modes in SARS-CoV-2 Protease Mpro

Shani Zev, Keren Raz, Renana Schwartz, Reem Tarabeh, Prashant Kumar Gupta and Dan T. Major

J. Chem. Inf. Model., 2021, 61, 2957
DOI: 10.1021/acs.jcim.1c00263

Searching for potential inhibitors of SARS-COV-2 main protease using supervised learning and perturbation calculations

Trung Hai Nguyen, Nguyen Minh Tam, Mai Van Tuan, Peng Zhan, Van V. Vu, Duong Tuan Quang and Son Tung Ngo

Chemical Physics, 2023, 564, 111709
DOI: 10.1016/j.chemphys.2022.111709

High-throughput virtual screening of potential inhibitors of GPR52 using docking and biased sampling method for Huntington’s disease therapy

Himanshi Gupta and Shakti Sahi

Mol Divers, 2024, 28, 3331
DOI: 10.1007/s11030-023-10763-y

Morusacerane: A new gammacerane triterpenoid from the trunk of Morus Alba linn. with α -glucosidase inhibitory activity

Hoang-Vinh-Truong Phan, Duy Vu Nguyen, Thi-Kim-Dung Le, Thi-Anh-Minh Nguyen, Phan-Si-Nguyen Dong, Thanh-Nha Tran, Ngoc-Van-Trang Dao, Hieu Cuong Nguyen, Hong Truong Luu, Warinthorn Chavasiri, Le-Thuy-Thuy-Trang Hoang and Van-Kieu Nguyen

Natural Product Research, 2025, 39, 4347
DOI: 10.1080/14786419.2024.2340043

Son Tung Ngo, Nguyen Minh Tam, Minh Quan Pham and Trung Hai Nguyen

J. Chem. Inf. Model., 2021, 61, 2302
DOI: 10.1021/acs.jcim.1c00159

In silico analysis to identify potential antitubercular molecules in Morus alba through virtual screening and molecular dynamics simulations

Mahvish Khan, Saif Khan, Freah L. Alshammary, Sama Zaidi, Vineeta Singh, Iqrar Ahmad, Harun Patel, Vijai Kumar Gupta and Shafiul Haque

Journal of Biomolecular Structure and Dynamics, 2024, 42, 1924
DOI: 10.1080/07391102.2023.2209648

Ethyl acetate extract of Smilax glabra Roxb roots and its major active compound astilbin promote osteoblastogenesis in vitro by upregulating bone cell differentiation- associated genes

Huyen T.T. Nguyen, Minh T.H. Nguyen, Thu X. Nguyen, Quan M. Pham, Ha X. Nguyen and Phuong T.M. Nguyen

Asian Pacific Journal of Tropical Biomedicine, 2021, 11, 553
DOI: 10.4103/2221-1691.331271

Can Antiviral Activity of Licorice Help Fight COVID-19 Infection?

Luisa Diomede, Marten Beeg, Alessio Gamba, Oscar Fumagalli, Marco Gobbi and Mario Salmona

Biomolecules, 2021, 11, 855
DOI: 10.3390/biom11060855

Calculation of binding affinity of JAK1 inhibitors via accurately computational estimation

Thi-Thuy-Huong Le, Linh Hoang Tran, Minh Tam Nguyen, Minh Quan Pham and Huong Thi Thu Phung

Journal of Biomolecular Structure and Dynamics, 2023, 41, 7224
DOI: 10.1080/07391102.2022.2118830

Assessing the ligand-binding affinity of chitinase inhibitors using steered-molecular simulations

Quynh Mai Thai, Huong TT Phung, Nguyen Thanh Tung, Linh Hoang Tran and Son Tung Ngo

Chemical Physics Letters, 2025, 864, 141899
DOI: 10.1016/j.cplett.2025.141899

Computational Determination of Potential Multiprotein Targeting Natural Compounds for Rational Drug Design Against SARS-COV-2

Ziyad Tariq Muhseen, Alaa R. Hameed, Halah M. H. Al-Hasani, Sajjad Ahmad and Guanglin Li

Molecules, 2021, 26, 674
DOI: 10.3390/molecules26030674

SARS-CoV-2 omicron RBD forms a weaker binding affinity to hACE2 compared to Delta RBD in in-silico studies

Hoa Thanh Le, Linh Hoang Tran and Huong Thi Thu Phung

Journal of Biomolecular Structure and Dynamics, 2024, 42, 4087
DOI: 10.1080/07391102.2023.2222827

Tinctoric acid A-B, two new hopan-type triterpenoids from the Vietnamese lichen, Parmotrema tinctorum (Despr. ex Nyl.) hale with α-glucosidase inhibitory activity

Le-Thuy-Thuy-Trang Hoang, Hoang-Vinh-Truong Phan, Hoai-Vu Nguyen-Si, Thanh-Nha Tran, Thi-Phi-Giao Vo, Huong Thi Thu Le, Ngoc-Van-Trang Dao, Thi-Minh-Suong Huynh, Dinh-Tri Mai, Phan-Si-Nguyen Dong and Van-Kieu Nguyen

Natural Product Research, 2025, 39, 3640
DOI: 10.1080/14786419.2024.2305659

Searching for AChE inhibitors from natural compounds by using machine learning and atomistic simulations

Quynh Mai Thai, T. Ngoc Han Pham, Dinh Minh Hiep, Minh Quan Pham, Phuong-Thao Tran, Trung Hai Nguyen and Son Tung Ngo

Journal of Molecular Graphics and Modelling, 2022, 115, 108230
DOI: 10.1016/j.jmgm.2022.108230

Upgrading nirmatrelvir to inhibit SARS-CoV-2 Mpro via DeepFrag and free energy calculations

Nguyen Minh Tam, Trung Hai Nguyen, Minh Quan Pham, Nam Dao Hong, Nguyen Thanh Tung, Van V. Vu, Duong Tuan Quang and Son Tung Ngo

Journal of Molecular Graphics and Modelling, 2023, 124, 108535
DOI: 10.1016/j.jmgm.2023.108535

Compromise in Docking Power of Liganded Crystal Structures of Mpro SARS-CoV-2 Surpasses 90% Success Rate

Dávid Zajaček, Adriána Dunárová, Lukas Bucinsky and Marek Štekláč

J. Chem. Inf. Model., 2024, 64, 1628
DOI: 10.1021/acs.jcim.3c01552