Current Computer-Aided Drug Design

Mechanisms Underlying the Attenuating Effects of Bugantang on Liver Fibrosis based on Network Pharmacology, Molecular Docking, and Molecular Dynamics Simulation
Zhang T, Chang J, Zheng Z, Chen G, Wu Y, Xiang J and Chen J
Liver fibrosis, a chronic liver disease, threatens people's health, increases the burden of healthcare, and currently lacks effective treatment measures. Bugantang (BGT) is a traditional Chinese herbal prescription from Jin Kui Yi with promising potential for treating liver fibrosis. Despite this potential, the efficacy and mechanism for treating liver fibrosis remain unclear.
Network Pharmacology and In Vivo Experimental Verification of the Mechanism of the Qing'e Pill for Treating Intervertebral Disc Degeneration
Jin H, Ma H, Wu J, Wu R, Xu H, Chen W, Li L, Zeng J and Wang F
The Qing'e Pill (QEP) is widely used to alleviate low back pain and sciatica caused by Intervertebral Disc Degeneration (IDD). However, its active components, key targets, and molecular mechanisms are not fully understood. The aim of this study is to elucidate the molecular mechanisms through which the QEP improves IDD using database mining techniques.
Xuebijing Exerts Protective Effects on Myocardial Cells by Upregulating TRIM16 and Inhibiting Oxidative Stress and Apoptosis
Meng X, Yan X, Xue P and Xi Z
This study utilized transcriptomic sequencing combined with cellular and animal models to explore the potential mechanisms of Xuebijing in treating sepsis-induced myocardial dysfunction, also known as sepsis-induced myocardial injury.
Study on the Mechanism of Alpinia officinarum Hance in the Improvement of Insulin Resistance through Network Pharmacology, Molecular Docking and in vitro Experimental Verification
Zhou M, Lian X, Zhang X, Xu J and Zhang J
Research has elucidated that the pathophysiological underpinnings of non-alcoholic fatty liver disease and type 2 diabetes mellitus are intrinsically linked to insulin resistance (IR). However, there are currently no pharmacotherapies specifically approved for combating IR. Although Alpinia officinarum Hance (A. officinarum) can ameliorate diabetes, the detailed molecular mechanism through which it influences IR has not been fully clarified.
Exploring the Potential Mechanisms of Danshen for the Treatment of Ulcerative Colitis based on Serum Pharmacochemistry, Gene Expression Profiling, and Network Pharmacology: Regulation of Cell Apoptosis and Inflammatory Response
Zhai RX, Wang MY, Du HT, Yan CX, Li ZW, Xu K, Li H, Fu XJ and Ren X
As a traditional Chinese medicine, Danshen shows potential efficacy for treating ulcerative colitis (UC). However, the bioactive components and mode of action were unclear.
Exploring the Mechanism of Centipeda minima in Treating Nasopharyngeal Carcinoma Based on Network Pharmacology
Huang C, Liu X, Wang W and Guo Z
Centipeda minima (CM) is a traditional Chinese herbal medicine used for the treatment of sinusitis and rhinitis, and it possesses anti-cancer properties. However, the mechanism of CM in the treatment of nasopharyngeal carcinoma (NPC) remains unclear.
Anti-Inflammatory Potential of Costus speciosus rhizome Bioactive Phytochemicals: A Combined GC-MS and Computational Approach Targeting TLR-4 Signaling
Raj A, Chakravorty A, Luktuke S, Santra S, Das S, Sahoo S, Ramesh K, A NF, Sana SS, Jayanthi S, Samanta A and Raghavan V
Plants represent a rich reservoir of bioactive compounds with established therapeutic value in diverse diseases. Notably, the Toll-like receptor-4 (TLR-4) signaling pathway plays a pivotal role in inflammation. Upon engagement with pro-inflammatory ligands like lipopolysaccharide, TLR-4 triggers downstream cascades involving nuclear factor ĸappa B and mitogen- activated protein kinases. This signaling cascade ultimately dictates the onset and progression of inflammatory diseases. Therefore, targeting TLR-4 signaling offers a promising therapeutic approach for managing inflammatory disorders.
Berberine Ameliorates High-fat-induced Insulin Resistance in HepG2 Cells by Modulating PPARs Signaling Pathway
Zhang L, Yang C, Ding X, Zhang H, Luan Y, Tang Y and Liu Z
Berberine (BBR), also known as berberine hydrochloride, was isolated from the rhizomes of the Coptis chinensis. Studies have reported that BBR plays an important role in glycolipid metabolism, including insulin (IR). The targets, and molecular mechanisms of BBR against hyperlipid-induced IR is worthy to be further studied.
Discovery of Two GSK3β Inhibitors from Sophora flavescens Ait. using Structure-based Virtual Screening and Bioactivity Evaluation
Pan D, Zeng Y, Jiang D, Zhang Y, Wu M, Huang Y, Han M and Jin XJ
Kushen (Sophora flavescens Ait.) has a long history of medicinal use in China due to its medicinal values, such as antibacterial, antiviral, and anti-inflammatory. Rapid discovery of the components and the medicinal effects exerted by Kushen will help elucidate the science of Kushen in curing diseases. GSK3β (glycogen synthase kinase-3 beta) is a protein kinase with a wide range of physiological functions, such as antibacterial, antiviral, and anti-inflammatory. The discovery of inhibitors targeting GSK3β from Kushen was not only helpful for the rapid discovery of the components responsible for the efficacy of Kushen but also important for the development of novel drugs.
Identifying Novel Inhibitors for Dengue NS2B-NS3 Protease by Combining Topological similarity, Molecular Dynamics, MMGBSA and SiteMap Analysis
Murtuja S, Siddique MUM, Srivastava KP, Agarwal YO, Wagh S, Yasmin S, Ansari A, Shaikh MS, Hasnain MS and Goyal SN
DENV NS2B-NS3 protease inhibitors were designed based upon the reference molecule, 4-(1,3-dioxoisoindolin-2-yl)-N-(4-ethylphenyl) benzenesulfonamide, reported by our team with the aim to optimize lead compound via rational approach. Top five best scoring molecules with zinc ids ZINC23504872, ZINC48412318, ZINC00413269, ZINC13998032 and ZINC75249613 bearing 'pyrimidin-4(3H)-one' basic scaffold have been identified as a promising candidate against DENV protease enzyme.
Synthesis, Biological Evaluation, Molecular Docking Studies and ADMET Prediction of Oxindole-Based Hybrids for the Treatment of Tuberculosis
Patel VP, Tripathi RKP and Mandal SD
With a projected mortality toll of 1.4 million in 2019, tuberculosis (TB) continues to be a significant public health concern around the world. Studies of novel treatments are required due to decreased bioavailability, increased toxicity, increased side effects, and resistance of several first- and second-line TB therapies, including isoniazid and ethionamide.
Decoding the Knacks of Ellagitannin Lead Compounds to Treat Nonalcoholic Fatty Liver Disease using Computer-aided Drug Designing
Shahid H, Ibrahim M, Alonazi WB and Chi Z
The prevalence of nonalcoholic fatty liver disease (NAFLD) is increasing globally, impacting individuals in Western nations and rapid growing in Asian countries due to sedentary lifestyles; thus, NAFLD has emerged as a significant worldwide health concern. Presently, lifestyle changes represent the primary approach to managing NAFLD.
Discovery of Novel PTP1B Inhibitors by High-throughput Virtual Screening
Debnath A, Rani A, Mazumder R, Mazumder A, Singh RK, Sharma S, Srivastava S, Chaudhary H, Mishra R, Khurana N, Sanchitra J and Jan SA
To Discover novel PTP1B inhibitors by high-throughput virtual screening Background: Type 2 Diabetes is a significant global health concern. According to projections, the estimated number of individuals affected by the condition will reach 578 million by the year 2030 and is expected to further increase to 700 million deaths by 2045. Protein Tyrosine Phosphatase 1B is an enzymatic protein that has a negative regulatory effect on the pathways involved in insulin signaling. This regulatory action ultimately results in the development of insulin resistance and the subsequent elevation of glucose levels in the bloodstream. The proper functioning of insulin signaling is essential for maintaining glucose homeostasis, whereas the disruption of insulin signaling can result in the development of type 2 diabetes. Consequently, we sought to utilize PTP1B as a drug target in this investigation.
Mechanisms Underlying the Protective Effects of Obeticholic Acid-Activated FXR in Valproic Acid-Induced Hepatotoxicity via Network Pharmacology, Molecular Docking, and Molecular Dynamics Simulations
Chen Y, Zhou J, Xu S and Wang L
Valproic acid (VPA)-induced hepatotoxicity is among the most common and severe adverse drug reactions, limiting its clinical application. Recent studies have suggested that activating the farnesoid X receptor (FXR) could be a promising therapeutic approach to alleviate VPA-induced hepatotoxicity; however, related research remains limited.
Computational Exploration of Isatin Derivatives for InhA Inhibition in Tuberculosis: Molecular Docking, MD Simulations and ADMET Insights
Patel VP, Tripathi RKP and Dharamsi A
Anti-tubercular drug discovery is a critical research area aimed at addressing the global health burden imposed by Mycobacterium tuberculosis. Nowadays, computational techniques have increased the likelihood of drug development compared to traditional, labor-intensive, and time-consuming drug design approaches. The pivotal goal of drug design is to identify compounds capable of selectively targeting protein, thereby disrupting its enzymatic activity. InhA, or NADH-dependent enoyl-acyl carrier protein reductase, stands at the forefront of targeted approaches in the battle against TB. Isatin derivatives have garnered interest for their diverse pharmacological activities.
Hybrid Class Balancing Approach for Chemical Compound Toxicity Prediction
Santiago-Gonzalez F, Martinez-Rodriguez JL, García-Perez C, Juárez-Saldivar A and Camacho-Cruz HE
Computational methods are crucial for efficient and cost-effective drug toxicity prediction. Unfortunately, the data used for prediction is often imbalanced, resulting in biased models that favor the majority class. This paper proposes an approach to apply a hybrid class balancing technique and evaluate its performance on computational models for toxicity prediction in Tox21 datasets.
In silico Discovery of Leptukalins, The New Potassium Channel Blockers from the Iranian Scorpion, Hemiscorpius Lepturus
Khalili-Salmasi M, Nazarian A, Amirkhani A, Mirzahoseini H and Bagheri KP
Blocking Kv 1.2 and Kv 1.3 potassium channels using scorpion venom- derived toxins holds potential therapeutic value. These channels are implicated in autoimmune diseases such as neurodegenerative diseases, multiple sclerosis, rheumatoid arthritis, and type 1 diabetes.
3D-QSAR, Pharmacophore Modeling, ADMET, and DFT Studies of Halogenated Conjugated Dienones as Potent MAO-B Inhibitors
Mathew GE, Herrera-Acevedo C, Scotti MT, Kumar S, Berisha A, Kaya S, Alfarraj S, Ansari MJ, Dhyani A, Sudevan ST, Kumar M and Mathew B
It has been reported that the extension of conjugation in chalcone scaffolds considerably enhanced the potency, selectivity, reversibility, and competitive mode of MAO-B inhibition. In this study, using the experimental results of IC50 values of fifteen halogenated conjugated dienone derivatives (MK1-MK15) against MAO-B, we developed a 3DQSAR model.
Antidepressant Properties of a Four-compound Cocktail Identified from Si-Ni-San by HIF-1 Pathway Modulation
An N, Zhang D, Xin J, Zhang X, Zhang Z, Ma L, Zhao L, Wu H, Feng W and Zheng X
Si-Ni-San (SNS) is the formula prescription of Traditional Chinese Medicine (TCM) with anti-depression properties, but its underlying mechanisms remain unclear.
Mechanism of in Treating Autism Spectrum Disorder Based on Network Pharmacology and Molecular Docking
Chen H, Zhou C, Li W and Bian Y
Recent epidemic survey data have revealed a globally increasing prevalence of autism spectrum disorders (ASDs). Currently, while Western medicine mostly uses a combination of comprehensive intervention and rehabilitative treatment, patient outcomes remain unsatisfactory. , used as a pair drug, positively affects the brain and kidneys, and can improve intelligence, wisdom, and awareness; however, the underlying mechanism of action is unclear.
Design, Screening, Synthesis, Characterisation and DFT-based Electronic Properties of Dihydropyridine-based Molecule as L-type Calcium Channel Blocker
Karmakar S, Basak HK, Paswan U, Saha S, Mandal SK and Chatterjee A
People of all nationalities and social classes are now affected by the growing issue of hypertension. Over time, there has been a consistent rise in the fatality rate. A range of therapeutic compounds, on the other hand, are often used to handle hypertension.