In Silico Prediction of New Inhibitors for Kirsten Rat Sarcoma G12D Cancer Drug Target Using Machine Learning-Based Virtual Screening, Molecular Docking, and Molecular Dynamic Simulation Approaches

Amar Ajmal, Muhammad Danial, Maryam Zulfat, Muhammad Numan, Sidra Zakir, Chandni Hayat, Khulood Fahad Alabbosh, Magdi E. A. Zaki, Arif Ali and Dongqing Wei

Pharmaceuticals, 2024, 17, 551
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Sanguinarine Induces ROS‐Mediated Mitochondrial Dysfunction and Inhibits AKT/GSK3 Signaling to Potentiate Apoptotic Effects in Cutaneous T‐Cell Lymphoma

Shilpa Kuttikrishnan, Muhammad Suleman, Fareed Ahmad, Zahwa Mariyam, Kalyani Patil, Rasheeda Anver, Abdul Q. Khan, Kirti S. Prabhu, Ajaz A. Bhat, Joerg Buddenkotte, Martin Steinhoff and Shahab Uddin

Phytotherapy Research, 2026
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Inhibition potential of natural flavonoids against selected omicron (B.1.19) mutations in the spike receptor binding domain of SARS-CoV-2: a molecular modeling approach

Anuj Kumar, Mansi Dutt, Budheswar Dehury, Gustavo Sganzerla Martinez, Cynthia L. Swan, Alyson A. Kelvin, Christopher D. Richardson and David J. Kelvin

Journal of Biomolecular Structure and Dynamics, 2025, 43, 1068
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HMPV-TherResDB: Comprehensive human metapneumovirus (HMPV) database for sequence-structure annotations, vaccine resources, and therapeutics research

Abbas Khan, Anwar Mohammad, Fahad M. Alshabrmi, Eid A. Alatawi, Muhammad Junaid and Abdelali Agouni

Virus Research, 2026, 363, 199665
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Identification of Drug Targets and Their Inhibitors in Yersinia pestis Strain 91001 through Subtractive Genomics, Machine Learning, and MD Simulation Approaches

Hamid Ali, Abdus Samad, Amar Ajmal, Amjad Ali, Ijaz Ali, Muhammad Danial, Masroor Kamal, Midrar Ullah, Riaz Ullah and Muhammad Kalim

Pharmaceuticals, 2023, 16, 1124
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Virus-like Plasmonic Nanoprobes for Quick Analysis of Antiviral Efficacy and Mutation-Induced Drug Resistance

Yuzhi Ouyang, Yancao Chen, Jinhui Shang, Shijie Sun, Xiangbin Wang, Shuangyan Huan, Bin Xiong and Xiao-Bing Zhang

Anal. Chem., 2023, 95, 5009
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Natural Compounds Targeting Thymic Stromal Lymphopoietin (TSLP): A Promising Therapeutic Strategy for Atopic Dermatitis

Muhammad Suleman, Chiara Moltrasio, Paola Maura Tricarico, Angelo Valerio Marzano and Sergio Crovella

Biomolecules, 2024, 14, 1521
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Animal models for COVID-19: advances, gaps and perspectives

Changfa Fan, Yong Wu, Xiong Rui, Yuansong Yang, Chen Ling, Susu Liu, Shunan Liu and Youchun Wang

Sig Transduct Target Ther, 2022, 7
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Exploring the natural products chemical space through a molecular search to discover potential inhibitors that target the hypoxia-inducible factor (HIF) prolyl hydroxylase domain (PHD)

Abrar Mohammad Sayaf, Saif Ullah Khalid, Jawad Ahmed Hameed, Abdulrahman Alshammari, Abbas Khan, Anwar Mohammad, Saeed Alghamdi, Dong-Qing Wei and KarKheng Yeoh

Front. Pharmacol., 2023, 14
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Structural and molecular investigation of the impact of S30L and D88N substitutions in G9R protein on coupling with E4R from Monkeypox virus (MPXV)

Yifan Jin, Syed Jawad Asad Gillani, Farah Batool, Fahad M. Alshabrmi, Eid A. Alatawi, Yasir Waheed, Anwar Mohammad, Abbas Khan and Dong-Qing Wei

Journal of Biomolecular Structure and Dynamics, 2025, 43, 1015
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Broad-Spectrum Small-Molecule Inhibitors of the SARS-CoV-2 Spike—ACE2 Protein–Protein Interaction from a Chemical Space of Privileged Protein Binders

Sung-Ting Chuang and Peter Buchwald

Pharmaceuticals, 2022, 15, 1084
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Exploring the hub gene CERS6 as a therapeutic target in type 1 diabetes through a bioinformatics and network analyst approach

Hassan Ayaz, Tajamul Hussain, Asia Nawaz, Muhammad Suleman, Salman Alrokayan, Dilber Uzun Ozsahin, Khalid Muhammad and Yasir Waheed

Sci Rep, 2025, 16
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Molecular screening of phytocompounds targeting the interface between influenza A NS1 and TRIM25 to enhance host immune responses

Muhammad Suleman, Abrar Mohammad Sayaf, Abbas Khan, Salman Ali Khan, Norah A. Albekairi, Abdulrahman Alshammari, Abdelali Agouni, Hadi M. Yassine and Sergio Crovella

Journal of Infection and Public Health, 2024, 17, 102448
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The apoptotic and anti‐proliferative effects of Neosetophomone B in T‐cell acute lymphoblastic leukaemia via PI3K/AKT/mTOR pathway inhibition

Shilpa Kuttikrishnan, Abdul W. Ansari, Muhammad Suleman, Fareed Ahmad, Kirti S. Prabhu, Tamam El‐Elimat, Feras Q. Alali, Ammira S. Al Shabeeb Akil, Ajaz A. Bhat, Maysaloun Merhi, Said Dermime, Martin Steinhoff and Shahab Uddin

Cell Proliferation, 2025, 58
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Structure-based molecular screening and dynamic simulation of phytocompounds targeting VEGFR-2: a novel therapeutic approach for papillary thyroid carcinoma

Shuai Wang, Lingqian Zhang, Wenjun Zhang, Xiong Zeng, Jie Mei, Weidong Xiao and Lijie Yang

Front. Pharmacol., 2025, 16
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Structure-Based Molecular Screening and Simulation Approaches To Inhibit Marburg Virus VP35 Protein Using Medicinal Phytocompounds for Restoring Host Immune Response

Mohammed A. Alshehri, Mohammed Alissa and Muhammad Suleman

J Pharm Innov, 2025, 20
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Targeting FGFR2 with natural products: Discovery and experimental validation of torosanin as a potent and selective therapeutic candidate for gallbladder cancer

Qingyun Wang, Chen Bai, Peng Zhang, Muhammad Suleman, Hailang Wei and Denggang Chen

International Journal of Biological Macromolecules, 2025, 322, 146888
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Discovery of Isojacareubin as a covalent inhibitor of SARS‐CoV‐2 main protease using structural and experimental approaches

Abbas Khan, Wang Heng, Kashif Imran, Guanghao Zhu, Jun Ji, Yani Zhang, Xiaoqing Guan, Guangbo Ge and Dong‐Qing Wei

Journal of Medical Virology, 2023, 95
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Integrative Machine Learning, Virtual Screening, and Molecular Modeling for BacA-Targeted Anti-Biofilm Drug Discovery Against Staphylococcal Infections

Ahmad Almatroudi

Crystals, 2024, 14, 1057
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Screening of medicinal phytocompounds with structure-based approaches to target key hotspot residues in tyrosyl-DNA phosphodiesterase 1: augmenting sensitivity of cancer cells to topoisomerase I inhibitors

Muhammad Suleman, Abbas Khan, Safir Ullah Khan, Mohammed Alissa, Suad A. Alghamdi, Amani Alghamdi, Abir Abdullah Alamro and Sergio Crovella

Journal of Biomolecular Structure and Dynamics, 2025, 43, 9442
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Benzimidazole compound abrogates SARS-COV-2 receptor-binding domain (RBD)/ACE2 interaction In vitro

Olaposi Omotuyi, Olusina M. Olatunji, Oyekanmi Nash, Babatunji Oyinloye, Opeyemi Soremekun, Ayodeji Ijagbuji and Segun Fatumo

Microbial Pathogenesis, 2023, 176, 105994
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AI Promoted Virtual Screening, Structure-Based Hit Optimization, and Synthesis of Novel COVID-19 S-RBD Domain Inhibitors

Ioannis Gkekas, Sotirios Katsamakas, Stelios Mylonas, Theano Fotopoulou, George Ε. Magoulas, Alia Cristina Tenchiu, Marios Dimitriou, Apostolos Axenopoulos, Nafsika Rossopoulou, Simona Kostova, Erich E. Wanker, Theodora Katsila, Demetris Papahatjis, Vassilis G. Gorgoulis, Maria Koufaki, Ioannis Karakasiliotis, Theodora Calogeropoulou, Petros Daras and Spyros Petrakis

J. Chem. Inf. Model., 2024, 64, 8562
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Molecular screening of natural compounds targeting KRAS(G12C): a multi-parametric strategy against acute lymphoblastic leukemia

Juan Peng, Kun Zheng, Lan Ren, Jingjing Cheng, Xuelian Feng and Ruibo Zhang

Journal of Enzyme Inhibition and Medicinal Chemistry, 2025, 40
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Ultra-Large-Scale Screening of Natural Compounds and Free Energy Calculations Revealed Potential Inhibitors for the Receptor-Binding Domain (RBD) of SARS-CoV-2

Lisha Guo, Faryar Zafar, Nawal Moeen, Fahad M. Alshabrmi, Junqi Lin, Syed Shujait Ali, Muhammad Munir, Abbas Khan and Dongqing Wei

Molecules, 2022, 27, 7317
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Unlocking the Therapeutic Potential of Alisertib in Breast Cancer: An In-Depth Exploration of Molecular Targets Using Network Pharmacology and Gene Expression Network

Suad A. Alghamdi, Mohammed Alissa and Muhammad Suleman

J Pharm Innov, 2025, 20
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Evaluation of 2-(1H-1,2,3-triazol-1-yl) acetic acid derivatives as potential human hypoxia-inducible factor (HIF) prolyl hydroxylase domain-2 (PHD2) inhibitors

Abrar Mohammad Sayaf, June Sun Cheah, Abbas Khan, Christopher J. Schofield, Abdelali Agouni and Kar Kheng Yeoh

Pure and Applied Chemistry, 2025, 97, 625
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Targeting 3Cpro of Enterovirus D68 with Medicinal Phytocompounds Using Structure-Based Molecular Screening and Molecular Simulation Approaches to Rescue the Host Immune Response

Muhammad Suleman, Abrar Mohammad Sayaf, Fazal Akbar, Mohammed Alissa, Ghadah S. Abusalim, Ghada M. Alnafesah, Kar Kheng Yeoh, Sergio Crovella and Hadi M. Yassine

J Pharm Innov, 2026, 21
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Structure-guided engineering and molecular simulations to design a potent monoclonal antibody to target aP2 antigen for adaptive immune response instigation against type 2 diabetes

Abbas Khan, Muhammad Ammar Zahid, Anwar Mohammad and Abdelali Agouni

Front. Immunol., 2024, 15
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Beta, Delta, and Omicron, Deadliest Among SARS-CoV-2 Variants: A Computational Repurposing Approach

Mohammad Mamun Alam, Sumaiya Binte Hannan, Tanvir Ahmed Saikat, Md Belayet Hasan Limon, Md Raihan Topu, Md Jowel Rana, Asma Salauddin, Sagar Bosu and Mohammed Ziaur Rahman

Evol Bioinform Online, 2023, 19
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Exploring the medicinal potential of Dark Chemical Matters (DCM) to design promising inhibitors for PLpro of SARS-CoV-2 using molecular screening and simulation approaches

Abbas Khan, Ayesha Liaqat, Adan Masood, Syed Shujait Ali, Liaqat Ali, Abdulrahman Alshammari, Abdullah F. Alasmari, Anwar Mohammad, Yasir Waheed and Dong-Qing Wei

Saudi Pharmaceutical Journal, 2023, 31, 101775
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Discovery of anti-methicillin-resistant Staphylococcus aureus inhibitors by targeting thymidylate kinase (TMPK) via multi-step virtual screening, molecular simulations, and free energy calculations

Talal Alshammari, Abdulrahman Alshammari, Metab Alharbi, Abdullah F. Alasmari, Abdullah S. Alhamed, Norah A. Albekairi, Alanoud Talal Aljasham and Amal F. Alshammary

Journal of Infection and Public Health, 2025, 18, 102884
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SARS-CoV-2 VOCs, Mutational diversity and clinical outcome: Are they modulating drug efficacy by altered binding strength?

Sheeba Saifi, Varsha Ravi, Sparsh Sharma, Aparna Swaminathan, Nar Singh Chauhan and Rajesh Pandey

Genomics, 2022, 114, 110466
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In silico formulation of a next-generation multiepitope vaccine for use as a prophylactic candidate against Crimean-Congo hemorrhagic fever

Rahat Alam, Abdus Samad, Foysal Ahammad, Suza Mohammad Nur, Ahad Amer Alsaiari, Raihan Rahman Imon, Md. Enamul Kabir Talukder, Zulkar Nain, Md. Mashiar Rahman, Farhan Mohammad and Tomasz M. Karpiński

BMC Med, 2023, 21
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Computational modeling of the effect of five mutations on the structure of the ACE2 receptor and their correlation with infectivity and virulence of some emerged variants of SARS-CoV-2 suggests mechanisms of binding affinity dysregulation

J.A. Rodriguez, J. Gonzalez, C.E. Arboleda-Bustos, N. Mendoza, C. Martinez and A. Pinzon

Chemico-Biological Interactions, 2022, 368, 110244
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Computational design of medicinal compounds to inhibit RBD-hACE2 interaction in the Omicron variant: unveiling a vulnerable target site

Muhammad Shahab, Shahina Akter, Md Murshed Hasan Sarkar, Tanjina Akhtar Banu, Barna Goswami, Sanjana Fatema Chowdhury, Showti Raheel Naser, Md Ahashan Habib, Aftab Ali Shaikh, Morteza Saki, Guojun Zheng and Md Salim Khan

Informatics in Medicine Unlocked, 2023, 40, 101281
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