Niyas Rehman

Methylglyoxal (MGO) is a metabolic byproduct of sugar metabolism involved in the formation of advanced glycation end products (AGEs) and its accumulation disrupts protein function, redox balance and cellular viability. Yet the metabolic rewiring required to divert MGO overflow and prevent these cytotoxic effects remains largely unknown. To address these gaps, we used flux sampling and flux balance analysis in genome scale metabolic model iJO1366 of E. coli . High glucose increased MGO flux from 0.16 mmol/gDCW/h to 1.87 mmol/gDCW/h in simulation. Large scale in silico screening of metabolic reactions identified that increasing threonine uptake, thereby increasing ethanol flux, reduced glucose induced increase in MGO flux from 1.87 mmol/gDCW/h to 0.405 mmol/gDCW/h. In silico inhibition of ethanol production (NAD ⁺ regeneration) inhibited the MGO lowering potential of threonine. Threonine supplementation actively drives the acetaldehyde to ethanol flux to provide localized NAD ⁺ relief, which subsequently enhances the flux of payoff phase in glycolysis (glyceraldehyde 3-phosphate), thereby efficiently draining the stagnated DHAP pool and shutting down the overflow towards MGO production. Unexpectedly, under reduced oxygen conditions, high glucose caused only a minimal increase in MGO flux, which was not reduced by threonine supplementation. Our study also decoded the mechanistic details behind this paradox. Though this model driven hypothesis requires further validation in vivo, these stoichiometric predictions have applications in metabolic engineering, for commercial MGO production. Furthermore, in vivo studies focused on bacterial stress, gut microbiome imbalances and AGE related diseases might benefit from these simulations. Figure

Introduction: Cardiovascular disease (CVD) is the leading cause of death worldwide and is substantially caused by high cholesterol levels. High levels of low-density lipoprotein cholesterol (LDL-C) lead to atherosclerosis, which greatly raises the risk of heart disease, such as heart attack, stroke, and so on. Therapeutic strategies for lowering cholesterol levels include the use of statins and PCSK9 inhibitors. To further reduce intestinal cholesterol absorption, the combination of ezetimibe with statin is an effective approach for controlling LDL-C levels and reducing cardiovascular disease risk. The Niemann-Pick C1-Like 1 (NPC1L1) protein is an important regulator of cholesterol absorption in the intestines and is a clinically proven target for lowering LDL-C levels. Although ezetimibe is prescribed for hypercholesterolemia, which blocks NPC1L1-mediated cholesterol absorption, its prolonged use could lead to hepatotoxicity, prompting the search for safer alternatives. Objective: To explore the interaction of ergosterol with NPC1L1 and assess its potential to modulate cholesterol absorption using in silico methods. Methods: Molecular docking, ADMET profiling, molecular dynamics (MD) simulations, post-MD analysis, and MM-PBSA binding free energy calculations were conducted to study ergosterol–NPC1L1 interactions and compare them with NPC1L1-ezetimibe and NPC1L1-cholesterol complex. Results: Docking and ADMET analyses revealed the existence of robust hydrophobic interaction of ergosterol with the binding pocket of NPC1L1 (binding energy −11.941 kcal/mol), identical to the binding of ezetimibe (−12.38 kcal/mol) and cholesterol (−11.432 kcal/mol), exhibiting comparable binding energies along with favourable pharmacokinetic properties. Molecular dynamics (MD) simulations and post-MD trajectory analyses suggest that the NPC1L1-ergosterol complex maintains structural stability during the simulation period. MM-PBSA binding free energy calculations consistently suggested a strong and stable interaction between NPC1L1-ergosterol (−27.61 ± 3.72 kcal/mol), comparable to that of NPC1L1-ezetimibe (−19.42 ± 4.87 kcal/mol) and NPC1L1-cholesterol (−32.53 ± 3.71 kcal/mol) complex. Conclusion: Our computational modelling studies suggested that ergosterol forms energetically favourable interactions with NPC1L1, hinting at its potential as a candidate for hypercholesterolemia and CVD management. However, comprehensive preclinical and clinical investigations are required to substantiate its therapeutic relevance.

Dopamine is an essential neurotransmitter found in both vertebrates and invertebrates which regulates motor coordination, cognition, emotional processing, and autonomic functions. Dopamine is biosynthesized from L-tyrosine and is primarily metabolized by catechol-O-methyltransferase (COMT), which regulates its concentration and ensures proper synaptic signalling within the basal ganglia. Dopamine deficiency, the hallmark of Parkinson’s disease, is a progressive neurodegenerative disorder caused by the loss of dopaminergic neurons in the substantia nigra pars compacta. To alleviate dopamine deficiency, current therapeutic strategies include administration of the dopamine precursor levodopa in combination with COMT inhibitors, which enhance levodopa bioavailability and prolong its therapeutic effect. However, the clinical utility of synthetic COMT inhibitors is often limited by hepatotoxicity and other adverse effects, underscoring the need for safer alternatives. In this context, plant-derived bioactive compounds are being increasingly investigated as potential inhibitors of COMT activity. Our study evaluated the affinity of 170 phytochemicals from Tamarindus indica against COMT utilizing computational strategies. Gallacetophenone, an aromatic ketone, was identified as a promising candidate that met the requirements for drug-likeness. Molecular dynamics (MD) simulations, supported by post-MDS analyses, principal component analysis, and free energy landscape analyses, demonstrated that gallacetophenone binding enhances the conformational stability of 3BWY compared to the control. These findings suggest that gallacetophenone may serve as a potential therapeutic phytochemical; however, its efficacy remains computationally predicted and requires validation through targeted in vitro and in vivo studies.

Klebsiella pneumoniae (K. pneumoniae) is a Gram-negative bacterium that causes severe community- and hospital-acquired infections. Its rising multidrug resistance complicates therapy, highlighting the need for novel drugs with broad-spectrum, multi-target potential. Leveraging the traditional use and therapeutic evidence of Sesbania grandiflora, this study performed structure-based computational screening of its phytochemicals against K. pneumoniae targets. Initially, 93 proteins with high annotation scores and resolved X-ray structures were identified. Six key therapeutic targets, including LpxH, fabG, KPC-2, GlmU, chbG, and ompA, were prioritized for their pathogenic role. Molecular docking revealed that 59 of 73 compounds interacted with all six targets with high affinity, while the remaining 14 compounds interacted with five targets. Network pharmacology indicated KPC-2, fabG, and ompA had the highest connectivity (73 compounds), followed by chbG and LpxH (72), and GlmU (61). ‘3′,6-di-O-feruloylsucrose’ had the strongest affinity for ompA, LpxH, and GlmU, while ‘Acarbose hydrate’ ranked top for chbG, fabG, and KPC-2. Out of 47 drug-like compounds, 9 passed ADMET filters. Sonchuionoside A was selected for molecular dynamics simulations, demonstrating stable binding to all targets. This suggests S. grandiflora phytoconstituents as multi-target regulators against K. pneumoniae and highlights Sonchuionoside A as a promising lead for further validation.

Regulatory backstage of cancer involves complex multifactorial mechanisms. Among these, the posttranscriptional modulation between microRNA (miRNAs) and mRNAs is implicated as major regulatory mechanisms in different cancers. The tissue- and disease-specific regulation of miRNAs by transcription factors (TFs) further adds to the complexity of this system potentially impacting cancer pathogenesis. To uncover the major TFs impacting miRNA transcription in cancer, the differentially expressed miRNAs and mRNAs in six different cancer types, namely, liver hepatocellular carcinoma, lung adenocarcinoma, prostate adenocarcinoma, stomach adenocarcinoma, breast invasive carcinoma, and colon adenocarcinoma, were compiled from The Cancer Genome Atlas. Using bioinformatics approaches and the TransmiR database, we assembled the 374 TFs that transcriptionally regulate miRNAs through repression mechanisms, and the negatively correlating TF-miR pairs in each cancer type. Importantly, we found that E2F1 and EZH2 , primarily linked with cell proliferation and cell cycle regulation, are potential regulators of miRNA transcription in cancers. The comprehensive TF-miR pairs in each cancer type uncovered in this study represent the unique and shared constituents that could functionally affect the cancer pathology. Understanding the mechanisms that regulate miRNA transcription in different cancers could help understand the pathology of cancer from a novel perspective with shared TFs constitutive to multiple cancers. This may also open up new avenues for cancer therapeutic innovation, in which miRNA-based interventions might be able to target and be relevant to multiple cancers at once in the future.

Erectile dysfunction (ED), a very commonly diagnosed disorder affecting millions of men, significantly diminishes quality of life and poses substantial psychosocial and physiological challenges. However, the currently available drugs and treatment strategies are often associated with undesirable side effects, further underscoring the need for safer and more effective therapeutic interventions. The development of phosphodiesterase type 5 (PDE5) inhibitors, such as Sildenafil, Tadalafil and Vardenafil, has revolutionized ED treatment but is associated with adverse effects, including headache, dizziness, vision disturbances and even cardiac issues. Safed Musli, Chlorophytum borivilianum, renowned for its aphrodisiac properties and traditional use in enhancing sexual health, has not been thoroughly studied for the toxicity and PDE5 inhibitory properties of its phytochemicals. This led to a comprehensive investigation aimed at better understanding its therapeutic potential. Among the 134 phytochemicals analyzed, Apigenin, a flavonoid, demonstrated a better binding affinity toward PDE5, having a dock score of −9.3 kcal/mol. The binding of Apigenin to PDE5 is illustrated with interactions like hydrogen bonds and van der Waals interactions, with a calculated binding free energy of [ ]7.76 ± 3.81 kcal/mol. In addition, comprehensive toxicity evaluations were conducted, confirming Apigenin’s favorable safety profile, including low toxicity and high gastrointestinal absorption, supporting its suitability for further drug development. Apigenin, a well-reported anti-inflammatory, antioxidant, antibacterial and antiviral compound found in various plants, shows promise as a natural PDE5 inhibitor with a favorable pharmacokinetic profile. Further validated by molecular dynamics simulations, reinforcing the potential of Apigenin as a viable drug candidate for the treatment of ED and warranting comprehensive in vitro and in vivo studies to confirm its therapeutic efficacy.

Hepatitis C virus (HCV) is a major global health burden affecting millions worldwide. A deeper understanding of and theories on the mechanisms of HCV replication and pathogenesis would bode well for diagnostics and therapeutics innovation. For example, HCV is known to modulate the host genes (e.g., human hepatocytes) for its efficient viral replication. These host genes are, therefore, among the major targets for treatment of HCV infection. We report here a systematic computational study that involved biocuration of published biomedical literature and data and subsequent network analyses to identify the potential microRNA-based therapeutics targeting HCV replication. We identified 539 HCV induced unidirectionally differential regulated miRNAs and assembled 115 genes that are positively/negatively associated with HCV replication. Furthermore, interaction networks by viral proteins were constructed to reveal the regulation of these microRNA (miRNA)-modulated genes. We found hsa-miR-191-5p and choline kinase alpha ( CHKA) as a significant microRNA-gene pair with relevance in glycerophospholipid metabolism, as validated by microarray expression profiles with temporal datasets. Altogether, these results provide comprehensive outline of the emerging data and hypotheses on the complex interplay between HCV and the host cells in modulating cellular miRNAs for viral proliferation. Our findings pave the way for the hypotheses that the induction of hsa-miR-191-5p or its delivery into hepatocytes or the inhibition of CHKA activity could be a potential therapeutic strategy to combat HCV-associated pathologies in the future.

Conventional pharmacological interventions for erectile dysfunction (ED) primarily rely on the phosphodiesterase-5 (PDE5) inhibitors such as sildenafil, tadalafil, vardenafil, and avanafil that have side effects despite their therapeutic effects. PDE5 is the primary cyclic guanosine monophosphate-degrading enzyme located in the smooth muscles of the corpus cavernosum in the penile tissue that helps in relieving erection. Natural products and phytochemicals are viable sources of molecular leads for drug discovery and development and, thus, offer prospects for innovation in ED treatment. This in silico study reports the screening of phytochemicals from the plant Tribulus terrestris with an eye to identify molecular candidates that inhibit PDE5. Natural products-based compounds that selectively target PDE5 are poised to be useful in clinical management of ED, and potentially with lesser side effects. The following top three phytochemicals identified from T. terrestris showed higher negative binding affinities for the PDE5 enzyme: diosgenin,dehydro (−11.1 kcal/mol), ruscogenin (−11.1 kcal/mol), and hecogenin (−10.3 kcal/mol) compared with the control drug sildenafil (−8.8 kcal/mol). Hydrogen bonds and Van der Waals interactions were the predominant forces influencing the interactions formed in the protein–ligand complexes. The ΔG _bind binding free energies for these top three phytochemicals, diosgenin,dehydro, ruscogenin, and hecogenin, were −19.99 ± 5.99 kcal/mol, −9.05 ± 5.16 kcal/mol, and −14.11 ± 5.33 kcal/mol, respectively. Importantly, diosgenin,dehydro, a saponin obtained from T. terrestris , was identified as a particularly promising candidate for PDE5 inhibition by virtue of its higher negative binding affinity and, therefore, displaying a potential in drug discovery and development for ED. In addition, in silico pharmacokinetic analysis and toxicity assessments support the prospects of these T. terrestris -derived phytochemicals for future in vitro and in vivo research for innovation in ED therapeutics.

Gastric cancer (GC) is the fifth most prevalent cancer worldwide, with Helicobacter pylori (H. pylori) infection as the leading cause. MicroRNAs (miRNAs), critical post-transcriptional regulators of gene expression, play pivotal roles in both H. pylori infection and GC pathogenesis. However, not all the dysregulated miRNAs exert a downstream effect on mRNAs, steering the pathologies. Utilising GEO datasets and literature curation, we compiled a comprehensive list of human differentially expressed (hDE) miRNAs in H. pylori-infected cell lines (HP-hDEmiRs) and GC tissues (GC-hDEmiRs). The identified targets of hDEmiRs from publicly available databases were compared with hDEmRNAs retrieved from GEO in each pathology to build a miRNA-mRNA network exhibiting inverse expression patterns, and the resultant miRNAs were considered as ‘Functional hDEmiRs’. Subsequently, 24 upregulated and 10 downregulated functional HP-hDEmiRs with 57 and 18 targets and 38 upregulated and 7 downregulated functional GC-hDEmiRs with 230 and 20 targets were identified, respectively. The miRNA-mRNA network of functional GC-hDEmiRs was validated using GC-hDEmRNAs from TCGA and a shared subset of functional hDEmiRs in H. pylori infection and GC was identified. This includes the upregulated hsa-miR-98-5p, hsa-miR-21-5p, hsa-let-7c-5p, hsa-let-7f-5p, hsa-let-7i-5p, hsa-miR-15a-5p, hsa-miR-181b-5p, hsa-miR-25-3p and the downregulated hsa-miR-204-5p, that could have a combinatorial effect in H. pylori infection to GC progression. Moreover, along with the TCGA-validated hydroxyacyl-CoA dehydrogenase (HADH), the epithelial splicing regulatory protein-2 (ESRP2) and dihydrolipoamide branched chain transacylase E2 (DBT) were downregulated in both conditions, possibly attributed to the effect of functional hDEmiRs targeting them. Our findings offer potential candidates for miRNA-directed therapeutics in these pathologies.

Camellia sinensis L. , commonly known as the tea plant, produces derivatives such as green tea, which are among the most extensively consumed beverages worldwide. Green tea is rich in polyphenolic compounds, such as epigallocatechin-3-gallate (EGCG) and gallocatechin gallate. These phytochemicals have drawn particular attention as antioxidants, especially in relation to their potential to reduce the risks for prostate cancer (PC) among other common human diseases. However, the molecular evidence base needs to be strengthened before large-scale controlled clinical trials with C. sinensis L. and/or specific phytochemicals are pursued. We investigated cytochrome P45017A1 (CYP17A1), a key enzyme in androgen biosynthesis, as a molecular target for the green tea phytochemicals. In this study, molecular docking, pharmacokinetic and toxicity evaluations, molecular dynamics (MD) simulations, and post-MD simulation analyses were performed to assess the binding potential of green tea phytochemicals with the CYP17A1 enzyme. A library of 92 green tea-derived phytochemicals, along with the reference inhibitor abiraterone, was docked against the CYP17A1 enzyme. MD simulations validated the stability and enhanced binding affinity of the CYP17A1–EGCG complex compared with the abiraterone complex, as further confirmed by post-MD simulation analyses. Collectively, these findings suggest that EGCG inhibits CYP17A1, potentially reducing androgen biosynthesis and thereby highlighting green tea as a promising natural source for PC therapeutics. Further preclinical and translational studies are warranted to substantiate the clinical applicability of green tea phytochemicals.