Browsing by Author "Nemat Ali"

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Anti-viral drug discovery against monkeypox and smallpox infection by natural curcumin derivatives: A Computational drug design approach
(Frontiers Media S.A., 2023) Shopnil Akash; Arafat Hossain; Md. Sarowar Hossain; Md. Mominur Rahman; Mohammad Z. Ahmed; Nemat Ali; Martin Valis; Kamil Kuca; Rohit Sharma
Background: In the last couple of years, viral infections have been leading the globe, considered one of the most widespread and extremely damaging health problems and one of the leading causes of mortality in the modern period. Although several viral infections are discovered, such as SARS CoV-2, Langya Henipavirus, there have only been a limited number of discoveries of possible antiviral drug, and vaccine that have even received authorization for the protection of human health. Recently, another virial infection is infecting worl dwi de (Monkeypox, and Smal l pox), whi ch concerns pharmaci sts, biochemists, doctors, and healthcare providers about another epidemic. Also, currently no specific treatment is available against Monkeypox. This research gap encouraged us to develop a new molecule to fight against monkeypox and smallpox disease. So, firstly, fifty different curcumin derivatives were collected from natural sources, which are available in the PubChem database, to determine antiviral capabilities against Monkeypox and Smallpox. Material and method: Preliminarily, the molecular docking experiment of fifty different curcumin derivatives were conducted, and the majority of the substances produced the expected binding affinities. Then, twelve curcumin derivatives were picked up for further analysis based on the maximum docking score. After that, the density functional theory (DFT) was used to determine chemical characterizations such as the highest occupied molecular orbital (HOMO), lowest unoccupied molecular orbital (LUMO), softness, and hardness, etc. Results: The mentioned derivatives demonstrated docking scores greater than 6.80 kcal/mol, and the most significant binding affinity was at-8.90 kcal/mol, even though 12 molecules had higher binding scores (-8.00 kcal/mol to-8.9 kcal/mol), and better than the standard medications. The molecular dynamic simulation is described by root mean square deviation (RMSD) and root-mean-square fluctuation (RMSF), demonstrating that all the compounds might be stable in the physiological system. Conclusion: In conclusion, each derivative of curcumin has outstanding absorpti on, di stri buti on, metabol i sm, excretion, and toxi ci ty (ADMET) characteristics. Hence, we recommended the aforementioned curcumin derivatives as potential antiviral agents for the treatment of Monkeypox and Smallpox virus, and more in vivo investigations are warranted to substantiate our findings. © 2023 Akash, Hossain, Hossain, Rahman, Ahmed, Ali, Valis, Kuca and Sharma.
Comprehensive Genomic, Mutation, Phylogenetic, and Statistical Analysis of the Monkeypox Virus Across Multiple Countries
(Springer, 2025) Imran Zafar; Faheem Kanwal; Muhammad Azmat; Ahsanullah UNAR; Ijaz Ali; Waqas Yousaf; Qurat Ul Ain; Mohd Ashraf Rather; Nemat Ali; Mohammad Rashid Khan; Amandeep K. Singh; Rohit Sharma
Our study offers a comprehensive Monkeypox virus (MPXV) analysis, utilizing innovative protocols to uncover potential vulnerabilities. We examine MPXV’s epidemiology, link to smallpox, genomics, mutation landscape, clinical features, diagnostics, therapeutics, FDA-approved drugs, clinical trials, and preventive strategies. We used various analytical methods to analyse genome data from the NCBI database (2019–2023) to assess sequence alignment, protein identification, and genome diversity. The phylogenomic analysis identified unique lineages and a mutation associated with human transmission, revealing that 24 MPXV proteins are particularly mutation-prone. Domain analysis confirmed conserved Ortho-poxvirus genes and critical regions, providing insights into MPXV’s structure, diversity, and host interaction. Additionally, we integrated clinical data, geospatial mapping, statistical analysis, and AI/ML for predictive insights on MPXV progression. We also explored bioinformatics tools and plant-based treatments, conducting in-silico studies to identify potential drug targets. Our research integrates epidemiological and genomic data to inform real-time preventive measures and optimize public health responses to MPXV. © Association of Microbiologists of India 2025.
Corrigendum: Anti-viral drug discovery against monkeypox and smallpox infection by natural curcumin derivatives: a computational drug design approach(Front. Cell. Infect. Microbiol., (2023), 13, (1157627), 10.3389/fcimb.2023.1157627)
(Frontiers Media S.A., 2023) Shopnil Akash; Arafat Hossain; Md. Sarowar Hossain; Md. Mominur Rahman; Mohammad Z. Ahmed; Nemat Ali; Martin Valis; Kamil Kuca; Rohit Sharma
In the published article, there was an error. The error in our article is in the abstract section. Before 6.8 kcal/mol, a minus (-) sign will be added and it will be -6.8 kcal/mol. A correction has been made to Abstract, Result, Three. “The mentioned derivatives demonstrated docking scores greater than 6.80 kcal/mol, and the most significant binding affinity was at -8.90 kcal/mol, even though 12 molecules had higher binding scores (-8.00 kcal/mol to -8.9 kcal/mol), and better than the standard medications”. The corrected sentence appears below: “The mentioned derivatives demonstrated docking scores greater than -6.80 kcal/mol, and the most significant binding affinity was at -8.90 kcal/mol, even though 12 molecules had higher binding scores (-8.00 kcal/mol to -8.9 kcal/mol), and better than the standard medications”. The authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. In the published article, there was an error. The 2nd error in our article is in the literature review section. The sub section 2.7 Effects of Curcumin on herpes simplex virus should be Effects of Curcumin on Hepatitis C virus instead of herpes simplex virus. A correction has been made to Literature review, Effects of Curcumin on herpes simplex virus, 0. “Effects of curcumin on herpes simplex virus”. The corrected sentence appears below: “Effects of Curcumin on Hepatitis C virus instead of herpes simplex virus”. The authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. Copyright © 2023 Akash, Hossain, Hossain, Rahman, Ahmed, Ali, Valis, Kuca and Sharma.
Deciphering the impact and mechanism of Trikatu, a spices-based formulation on alcoholic liver disease employing network pharmacology analysis and in vivo validation
(Frontiers Media S.A., 2022) Ruchi Sharma; Mangala Jadhav; Neha Choudhary; Arun Kumar; Abdur Rauf; Rohit Gundamaraju; Abdullah F. AlAsmari; Nemat Ali; Rajeev K. Singla; Rohit Sharma; Bairong Shen
Trikatu Churna (TC) comprising Zingiber officinale rhizome, Piper longum, and Piper nigrum fruit, is effective in treating liver diseases and has high nutraceutical values. However, the efficacy of TC in treating alcoholic liver disease (ALD) and its mechanism remain largely unknown. This study evaluated the hepatoprotective effects of different doses of TC as well as to identify the bioactive components and determine their mechanism of action against ethanol-induced ALD. A compound-target network analysis model of TC was established to identify its potential bioactive compounds and pathways that might regulate its hepatoprotective effects. Further, in-vivo studies were performed to validate the potential of TC (200 mg/kg and 400 mg/kg b.w.) in the treatment and management of ALD. The study revealed that both the dosages of TC demonstrate significant (p > 0.0001) hepatoprotective effects by improving body weight, total bilirubin, serum glutamic oxaloacetic transaminase (SGOT), serum glutamic pyruvic transaminase (SGPT), serum alkaline phosphate (ALP), total cholesterol, total protein, globulin, albumin, and liver morphology. The High-performance thin-layer chromatography (HPTLC) fingerprinting of TC showed the presence of piperine. Network pharmacology identifies the role of TC in regulating various signaling processes including Advanced glycation end products-receptor for advanced glycation end products (AGE-RAGE), Hypoxia-inducible factors (HIF-1), Nuclear factor kappa-light-chain-enhancer of activated B cells (NF-Kappa B), and Phosphatidylinositol 3-kinase/protein kinase B (PI3K/Akt) signaling to exert its anti-inflammatory, antioxidant and anti-apoptotic role in managing ALD. Based on the bioinformatics analysis, some of the key targets of TC were found to be Prostaglandin-Endoperoxide Synthase 2 (PTGS2) or Cyclooxygenase-2 (COX-2), Sirtuin 1 (SRT1), and caspase-3. These effects may serve as a novel therapeutic option for the treatment of ALD. These preclinical validation studies for the ethnopharmacological potential of TC in ALD treatment further paved the way for researchers to perform next-level translational and clinical studies. Further, in-depth experimental studies for the validation of these bioinformatics-based results will give a clearer picture of mechanisms. Copyright © 2022 Sharma, Jadhav, Choudhary, Kumar, Rauf, Gundamaraju, AlAsmari, Ali, Singla, Sharma and Shen.
IL-8 polymorphisms (−251T/A, −1633T/C) and their effects on COVID-19 clinical outcomes: An observational study
(Academic Press, 2025) Hari Om Singh; Josna Wilson; Goldi Namdev; Meenakshi Bhattacharya; Anchal Pratap Singh; Supriya D. Mahajan; Nemat Ali; Abdullah F. Alasmari
Background: COVID-19 presents with a wide spectrum of clinical outcomes, ranging from asymptomatic infection to critical illness. The cytokine storm is a hallmark of severe COVID-19 and is associated with elevated levels of pro-inflammatory cytokines, often observed in severe cases. Genetic polymorphisms in the IL-8 gene may influence individual responses to SARS-CoV-2 infection and the severity of the disease. Methods: A case-control study was conducted involving 200 COVID-19 patients and 201 healthy controls. Two IL-8 gene polymorphisms, −251T/A and +1633T/C, were genotyped using the PCR-RFLP (Polymerase chain reaction-restriction fragment length polymorphism) technique. Results: The IL-8 -251TA genotype and −251A allele were significantly associated with COVID-19 patients (P = 0.02, OR = 2.31; P = 0.03, OR = 1.38). The AT haplotype (−251A/+1633C) showed a non-significant trend toward increased risk for COVID-19 (P = 0.11, OR = 2.24). The IL-8 +1633 TT genotype was associated with impaired platelet counts among COVID-19 patients (P = 0.05, OR = 2.42). The IL-8 -251TA genotype was significantly associated with all stages of COVID-19 severity-critical (P = 0.05, OR = 8.15), severe (P = 0.002, OR = 2.74), moderate (P = 0.008, OR = 2.16), and mild (P = 0.01, OR = 2.89). In contrast, the IL-8 -251AA genotype was significantly associated with the critical stage (P = 0.04, OR = 2.53). A marginally significant association was observed between the IL-8 +1633CT genotype and the severe stage of COVID-19 (P = 0.07, OR = 2.13). Additionally, a borderline significant association was noted between elevated serum creatinine levels and the IL-8 -251AA genotype (P = 0.07, OR = 2.45). Conclusion: The IL-8 -251T/A polymorphism may serve as a potential risk factor for severe disease progression; the +1633 TT genotype may be linked to thrombocytopenia and poor clinical outcomes; and the −251AA genotype may be associated with elevated serum creatinine levels and an increased risk of renal dysfunction. © 2025 Elsevier Ltd
In-Silico Investigation on the Inhibitory Effect of Compounds from Essential Oils of Boesenbergia rotunda on Sortase-A of Streptococcus mutans
(Elsevier B.V., 2024) Ngoc NH Pham; Tran Trung Hieu; Rita Dadarao Chakole; Sudarshana Borah; Nikita Gaikwad; Shailejkumar D Bonde; Devesh Sharma; Shilpa Sudhakar Harak; Savita Shrikant Deokar; Kiran Ashok Ingole; Mohamed Mohany; Nemat Ali; Nobendu Mukerjee; Arabinda Ghosh; Rohit Sharma
Streptococcus mutans (S. mutans), a bacterium involved in tooth decay, utilizes the enzyme sortase-A (Srt-A) to anchor surface proteins and form biofilms, aiding in its adhesion to tooth surfaces. However, the emergence of resistance to existing inhibitors necessitates the search for novel treatment options. This study employed virtual screening methods to identify potential inhibitors, focusing on compounds derived from the essential oils of Boesenbergia rotunda.Gas chromatography with mass spectroscopy (GC-MS) identified 18 compounds and out of them, identified top five compounds with the lowest docking scores. Simulations based on molecular dynamics (MD) were then executed for investigating the extent of stability shown by the resulting complexes. Furthermore, the compound's pharmacological properties were evaluated using absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis. Findings unveiled a multitude of compounds, including Nerol, (1E)-[(2,4-Dinitrophenyl) (phenyl)methylene] hydrazine, and Chloromethyl 2-chlorodecanoate, which demonstrated favorable affinities, appropriate pharmacokinetic parameters, and the ability to form hydrogen bonds with Cys205, thus making them potential inhibitors to disrupt the catalytic activity of SrtA. Notably, Hemanthidine exhibited a high binding affinity of -9.22 kcal/mol, and found better than standard curcumin -5.62 kcal/mol. Moreover, its carbonyl group may play a crucial role in impeding biofilm formation. These promising results provide a basis for further research in developing effective treatments for bacterial infections, specifically targeting tooth decay. © 2024 SAAB
Mechanistic inhibition of gastric cancer-associated bacteria Helicobacter pylori by selected phytocompounds: A new cutting-edge computational approach
(Elsevier Ltd, 2023) Shopnil Akash; Imren Bayıl; Sajjat Mahmood; Nobendu Mukerjee; Tamanna Akter Mili; Kuldeep Dhama; Md Anisur Rahman; Swastika Maitra; Mohamed Mohany; Salim S. Al-Rejaie; Nemat Ali; Prabhakar Semwal; Rohit Sharma
Background: Helicobacter pylori (H. pylori) is a persistent bacterial inhabitant in the stomachs of approximately half the global populace. This bacterium is directly linked to chronic gastritis, leading to a heightened risk of duodenal and gastric ulcer diseases, and is the predominant risk factor for gastric cancer - the second most common cause of cancer-related deaths globally. The increasing prevalence of antibiotic resistance necessitates the exploration of innovative treatment alternatives to mitigate the H. pylori menace. Methods: Initiating our study, we curated a list of thirty phytochemicals based on previous literature and subjected them to molecular docking studies. Subsequently, eight phytocompounds—Glabridin, Isoliquiritin, Sanguinarine, Liquiritin, Glycyrrhetic acid, Beta-carotin, Diosgenin, and Sarsasapogenin—were meticulously chosen based on superior binding scores. These were further subjected to an extensive computational analysis encompassing ADMET profiling, drug-likeness evaluation, principal component analysis (PCA), and molecular dynamic simulations (MDs) in comparison with the conventional drug, Mitomycin. Results: The natural compounds investigated demonstrated superior docking affinities to H. pylori targets compared to the standard Mitomycin. Notably, the phytocompounds Diosgenin and Sarsasapogenin stood out due to their exceptional binding affinities and pharmacokinetic properties, including favorable ADMET profiles. Conclusion: Our comprehensive and technologically-advanced approach showcases the potential of identified phytocompounds as pioneering therapeutic agents against H. pylori-induced gastric malignancies. In light of our promising in silico results, we recommend these natural compounds as potential candidates for advancing H. pylori-targeted drug development. Given their potential, we strongly advocate for subsequent in vitro and in vivo studies to validate their therapeutic efficacy against this formidable gastrointestinal bacterium. © 2023