đź“„ Research Papers
In silico evaluation of Ocimum sanctum phytochemicals for diabetic foot ulcer therapy through docking, ADMET, DFT, and molecular dynamics
Authors: Sk. Faisal Ahmed, Md. Raihan Ahmed, Md. Faisal Patwary Hemal, Faria Mehjabin Chandni, Tousif Arafat Rafsan, Susmoy Sarker, Jaikee Kumar Singh, Krishan Kant Meena, Kajal Arora6 & Abhishek Kumar Verma
Journal: Nature Scientific Reports
Publication Date: Dec. 2, 2025
This study explores the potential of phytocompounds derived from Ocimum sanctum (Holy Basil) to accelerate the healing of diabetic foot ulcers (DFUs). The research targets MMP-9, an enzyme found in elevated levels in DFUs that delays wound repair. Through computational analysis—including molecular docking, ADME toxicity screening, and molecular dynamics simulations—the study identifies apigenin as a superior, stable, and drug-like inhibitor compared to the control drug, (R)-ND-336.
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Cheminformatics-based analysis identified Novel compounds from Nelumbo nucifera as potential inhibitors targeting PI3k/Akt/mTOR Pathway of HR+/HER2- subtype for Breast Cancer
Authors: Sk Faisal Ahmed, Proja Barua, Md Al Amin, Rahnuma Tabassum, Mir Mohammad Ehsanul Haque, Lamia Islam, Md Shohel Hossain, Abhishek Kumar Verma
Journal: Biochemical and Biophysical Research Communications
Publication Date: Nov. 12, 2025
The present study investigates the in-silico identification of novel phytochemical inhibitors from N. nucifera molecularly targeting the PI3K/Akt/mTOR signalling pathway as a breast cancer chemotherapeutic agent, especially to treat PIK3CA mutant tumours. Despite huge advancements, including the application of various complex intracellular signalling pathways in oncogenesis, breast cancer remains a menace, causing significant morbidity and mortality worldwide.
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Computational analysis of miRNA mediated KDR gene regulation and natural VEGFR2 inhibitors from Persicaria hydropiper in hepatocellular carcinoma
Authors: Sk Faisal Ahmed, Sunbin Samin, Amalesh Mondal, Md Fahim Islam, Hafiza Akter Laboni, Azmin Alam Ela, Tithi Mondal
Journal: Nature Scientific Reports
Publication Date: Oct. 30, 2025
Liver cancer is one of the deadliest cancers worldwide. There is a growing need for natural therapeutic options due to the rising global morbidity incidence of liver cancer. Due to its crucial function in angiogenesis, vascular endothelial growth factor (VEGF) signaling is considered as an ideal target for therapeutic intervention. In this in silico study, we have screened 16 microRNAs (miRNAs) that target the KDR gene, which encode VEGFR-2, and 113 natural compounds derived from Persicaria hydropiper for their anti-angiogenic properties.
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Licoisoflavone B and glabridin from Glycyrrhiza glabra as potent nucleoprotein antagonists of Lassa virus: insights from molecular docking, dynamics simulation, PCA, and DFT studies
Authors: Sk. Faisal Ahmed , Md. Masudur Rahman Munna, Md. Hossain Ahme , Md. Mostafizur Rahman, Minhajul Islam, Esha Mony Bristy
Journal: Journal of Genetic Engineering and Biotechnology
Publication Date: Aug. 5, 2025
Lassa virus, a deadly pathogen in West and Central Africa with no available vaccine and limited treatment options, urgently requires new therapies. This study screened 69 phytochemicals from Glycyrrhiza glabra and identified licoisoflavone B and glabridin as promising inhibitors of the viral nucleoprotein, crucial for replication and immune evasion. Both compounds showed strong binding affinities, favorable ADMET profiles, and structural stability in 100 ns molecular dynamics simulations, further supported by principal component and density functional theory analyses. These findings highlight licoisoflavone B and glabridin as potential anti-Lassa virus drug candidates, warranting further experimental validation.
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In silico identification of promising PD-L1 inhibitors from selected indian medicinal plants for treatment of triple negative breast cancer
Authors: Sk. Faisal Ahmed, Md. Shohel Hossain, Amalesh Mondal, Musab Shahariar, Shormila Akter Sumya, Nahid Sultan Rizu, Lamia Hasan Joarder Barsha
Journal: Plosone
Publication Date: July 10, 2025
Triple-negative breast cancer (TNBC) is a highly aggressive subtype with limited therapeutic targets and poor survival outcomes. Given the limitations of antibody-based PD-1/PD-L1 therapies, this study explored small-molecule phytochemicals as potential PD-L1 inhibitors. A virtual screening of 953 compounds from eleven Indian medicinal plants identified 4-hydroxychalcone (from Glycyrrhiza glabra) and flavylium (from Catharanthus roseus) as top candidates with strong binding affinities, favorable ADMET properties, and high stability in molecular dynamics simulations. Both compounds showed enhanced gastrointestinal absorption and no predicted toxicity, making them promising leads for novel PD-L1 inhibitor development in TNBC therapy, though further experimental validation is required.
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In Silico Identification of Emblica officinalis Compounds Inhibiting Thermolabile Hemolysin from Vibrio alginolyticus in Shrimp
Authors: Sayed Mashequl Bari, Meamaching Marma, Nafees Bin Reza, Sk. Faisal Ahmed, Shoriful Islam, Nafis Rayhan, Md. Alomgir Hossian, Md. Matiur Rahman and Md. Saiful Alam
Journal: Current Computer-Aided Drug Design
Publication Date: Feb. 18, 2025
Vibrio alginolyticus is a major pathogen in shrimp aquaculture, and reliance on antibiotics raises concerns about resistance. This study used computational approaches to explore garlic (Allium sativum) compounds as alternatives for inhibiting the virulence protein thermolabile hemolysin. Among 35 tested compounds, protopine, gibberellin A7, and gibberellic acid showed the strongest binding affinities, with gibberellin A7 and gibberellic acid demonstrating favorable pharmacokinetics, low toxicity, and high stability in molecular dynamics simulations. These findings suggest that garlic-derived compounds, particularly gibberellin A7 and gibberellic acid, may serve as promising candidates to combat shrimp vibriosis, pending further in vitro and in vivo validation.
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Synthesis, antiviral activity, molecular docking, and molecular dynamics studies of ethoxy phthalimide pyrazole derivatives against Cytomegalovirus and Varicella-Zoster virus: potential consequences and strategies for developing new antiviral treatments
Authors: Abhishek Kumar Verma, Vipin Yadav, Ali Asger Bhojiya, Sudhir K. Upadhyay, Nripendra Singh, Shruti Shree Pareek, Mohammad Ashid, Sk. Faisal Ahmed, Md. Shahadat Hossain
Journal: Journal of Biomolecular Structure and Dynamics
Publication Date: Nov. 15, 2023
This research investigates the synthesis and antiviral properties of ethoxy phthalimide pyrazole derivatives against Cytomegalovirus and Varicella-Zoster virus. Molecular docking and dynamics studies assess the interaction between these derivatives and viral targets, aiming to develop new antiviral treatments.
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Synthesis, antiviral activity, molecular docking, and molecular dynamics studies of ethoxy phthalimide pyrazole derivatives against Cytomegalovirus and Varicella-Zoster virus: potential consequences and strategies for developing new antiviral treatments
Authors: Abhishek Kumar Verma, Vipin Yadav, Ali Asger Bhojiya, Sudhir K. Upadhyay, Nripendra Singh, Shruti Shree Pareek, Mohammad Ashid, Sk. Faisal Ahmed, Md. Shahadat Hossain
Journal: Journal of Biomolecular Structure and Dynamics
Publication Date: Nov. 15, 2023
Substituted ethoxy phthalimide pyrazole derivatives (6a–e) were synthesized and evaluated for antiviral potential against CMV and VZV. Docking and in vitro studies showed strong, stable binding to key viral proteins, with higher binding energies than standard drugs Ganciclovir and Acyclovir. ADME/T analysis indicated low toxicity, suggesting these compounds as promising multitarget inhibitors and potential adjuvant therapies for CMV and VZV infections.
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