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Design, Synthesis, Antitumor Activity Evaluation, and Molecular Dynamics Simulation of Some 2-Aminopyrazine Derivatives Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2024-03-15 Hangrui Cui, Ruifeng Zhang, Xin Xiong, Zhiwen Cui, Zhijian Min, Jinglong Liu, Xunping Li, Zhenli Min
Objective:: Cancer poses a great threat to human health, and effective drugs to treat it are always needed. Several compounds containing a 2-aminopyrazine framework have been identified as antitumor agents with SHP2 inhibition activities. This current work aimed to search for more potent novel compounds possessing a 2-aminopyrazine moiety with antitumor activities. Methods:: A series of 12 novel 2-aminopyrazine
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Chemical Synthesis, Biological Evaluation, and Cheminformatics Analysis of a Group of Chlorinated Diaryl Sulfonamides: Promising Inhibitors of Cholesteryl Ester Transfer Protein Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2024-03-01 Reema Abu Khalaf, Ala’a Lafi, Rima Hajjo, Mahmoud A. Al-Sha'er
Background: Hyperlipidemia is characterized by an abnormally elevated serum cholesterol, triglycerides, or both. The relationship between an elevated level of LDL and cardiovascular diseases is well-established. Cholesteryl ester transfer protein (CETP) is an enzyme that moves cholesterol esters and triglycerides between LDL, VLDL, and HDL. CETP inhibition leads to a reduction in cardiovascular disease
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Exploring the Mechanisms of Sanguinarine in the Treatment of Osteoporosis by Integrating Network Pharmacology Analysis and Deep Learning Technology Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2024-02-22 Yonghong Tang, Daoqing Zhou, Fengping Gan, Zhicheng Yao, Yuqing Zeng
Background:: Sanguinarine (SAN) has been reported to have antioxidant, antiinflammatory, and antimicrobial activities with potential for the treatment of osteoporosis (OP). Objective:: This work purposed to unravel the molecular mechanisms of SAN in the treatment of OP. Methods:: OP-related genes and SAN-related targets were predicted from public databases. Differential expression analysis and VennDiagram
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Natural Compound Dioscin Targeting Multiple Cancer Pathways through its High Affinity Binding to B Cell Lymphoma-2 Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2024-02-20 Shweta Gulia, Prakash Chandra, Asmita Das
Objective:: The study aimed to explore the crucial genes involved in cancer-related biological processes, including EMT, autophagy, apoptosis, anoikis, and metastasis. It also sought to identify common genes among the pathways linked to these biological processes, determine the level of Bcl-2 expression in various types of cancers, and find a potent inhibitor of Bcl-2 among natural compounds. Methods::
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WSHNN: A Weakly Supervised Hybrid Neural Network for the Identification of DNA-Protein Binding Sites Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2024-02-13 Wenzheng Bao, Baitong Chen, Yue Zhang
Introduction: Transcription factors are vital biological components that control gene expression, and their primary biological function is to recognize DNA sequences. As related research continues, it was found that the specificity of DNA-protein binding has a significant role in gene expression, regulation, and especially gene therapy. Convolutional Neural Networks (CNNs) have become increasingly
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Uncovering the Mechanisms of Cinnamic Acid Treating Diabetic Nephropathy Based on Network Pharmacology, Molecular Docking, and Experimental Validation Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2024-02-13 Limiao Dai, Yang He, Siqiang Zheng, Jiyu Tang, Lanjun Fu, Li Zhao
Background: Cinnamic acid (Cinn) is a phenolic acid of Cinnamomum cassia (L.) J. Presl. that can ameliorate diabetic nephropathy (DN). However, comprehensive therapeutic targets and underlying mechanisms for Cinn against DN are limited. Objective: In this study, a network pharmacology approach and in vivo experiments were adopted to predict the pharmacological effects and mechanisms of Cinn in DN therapy
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Exploration of Fingerprints and Data Mining-based Prediction of Some Bioactive Compounds from Allium sativum as Histone Deacetylase 9 (HDAC9) Inhibitors Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2024-02-07 Totan Das, Arijit Bhattacharya, Tarun Jha, Shovanlal Gayen
Background: Histone deacetylase 9 (HDAC9) is an important member of the class IIa family of histone deacetylases. It is well established that over-expression of HDAC9 causes various types of cancers including gastric cancer, breast cancer, ovarian cancer, liver cancer, lung cancer, lymphoblastic leukaemia, etc. The important role of HDAC9 is also recognized in the development of bone, cardiac muscles
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Status and Prospects of Research on Deep Learning-based De Novo Generation of Drug Molecules Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2024-02-07 Huanghao Shi, Zhichao Wang, Litao Zhou, Zhiwang Xu, Liangxu Xie, Ren Kong, Shan Chang
: Traditional molecular de novo generation methods, such as evolutionary algorithms, generate new molecules mainly by linking existing atomic building blocks. The challenging issues in these methods include difficulty in synthesis, failure to achieve desired properties, and structural optimization requirements. Advances in deep learning offer new ideas for rational and robust de novo drug design. Deep
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Exploring the Molecular Mechanism by which Kaempferol Attenuates Sepsis-related Acute Respiratory Distress Syndrome Based on Network Pharmacology and Experimental Verification Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2024-02-07 Weichao Ding, Changbao Huang, Juan Chen, Wei Zhang, Mengmeng Wang, Xiaohang Ji, Shinan Nie, Zhaorui Sun
Background: Sepsis-related acute respiratory distress syndrome (ARDS) is a fatal disease without effective therapy. Kaempferol is a flavonoid compound extracted from natural plant products; it exerts numerous pharmacological effects. Kaempferol attenuates sepsis-related ARDS; however, the underlying protective mechanism has not been elucidated completely. Objective: This study aimed to use network
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Mechanism of the Effect of Scopolamine on Breast Cancer: Determination by Network Pharmacology and Bioinformatics Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2024-02-04 Yang Xiao, Qiang Guo, Yichen Li, Mengcong Ma, Yu Sun, Qing Gu, Yunfeng Xiao
Background: To a certain extent, traditional Chinese medicine (TCM)-based anesthesia has replaced opiate administration in recent years. Preliminary drug screening has revealed that scopolamine may affect breast cancer (BC) metastasis by an unknown mechanism. Methods: Network pharmacology, bioinformatics, and protein-protein interaction (PPI) topological analysis were implemented to identify the core
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Insights to Design New Drugs against Human African Trypanosomiasis Targeting Rhodesain using Covalent Docking, Molecular Dynamics Simulations, and MM-PBSA Calculations Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2024-02-04 Igor José dos Santos Nascimento, Mirelly Barbosa Santos, Washley Phyama De Jesus Marinho, Ricardo Olimpio de Moura
Background:: Neglected tropical diseases (NTDs) are parasitic and bacterial diseases that affect approximately 149 countries, mainly the poor population without basic sanitation. Among these, African Human Trypanosomiasis (HAT), known as sleeping sickness, shows alarming data, with treatment based on suramin and pentamidine in the initial phase and melarsoprol and eflornithine in the chronic phase
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Comprehensive In Silico Analysis of Uncaria Tomentosa Extract: Chemical Profiling, Antioxidant Assessment, and CLASP Protein Interaction for Drug Design in Neurodegenerative Diseases Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2024-02-04 Sanjesh Kumar, Siva Prasad Panda
Background:: Uncaria tomentosa is a traditional medicinal herb renowned for its anti-inflammatory, antioxidant, and immune-enhancing properties. In the realm of neurodegenerative diseases (NDDS), CLASP proteins, responsible for regulating microtubule dynamics in neurons, have emerged as critical players. Dysregulation of CLASP proteins is associated with NDDS, such as Alzheimer's, Parkinson's, and
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Astragaloside IV Overcomes Anlotinib Resistance in Non-small Cell Lung Cancer through miR-181a-3p/UPR-ERAD Axis Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2024-02-04 Lihuai Wang, Tonglin Sun, Xiao Yang, Zhi Wen, Yinhui Sun, Hua Liu
Background:: Astragaloside IV (AS-IV) has been shown to have a curative effect on non-small cell lung cancer (NSCLC). This study aimed to elucidate the role of AS-IV in NSCLC cell anlotinib resistance (AR). Methods:: The NSCLC/AR cells, resistant to anlotinib, have been produced. The role of AS-IV in the AR of NSCLC cells about the miR-181a-3p/unfolded protein response (UPR)- endoplasmic reticulum
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AI-based Virtual Screening of Traditional Chinese Medicine and the Discovery of Novel Inhibitors of TCTP Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2024-02-04 Juxia Bai, Yangyang Ni, Yuqi Zhang, Junfeng Wan, Liqun Liang, Haoran Qiao, Yanyan Zhu, Qingjie Zhao, Huiyu Li
Background: Translationally controlled tumour protein (TCTP) is associated with tumor diseases, such as breast cancer, and its inhibitor can reduce the growth of tumor cells. Unfortunately, there is currently no effective medication available for treating TCTP-related breast cancer. Objective: The objective of this study was to explore the inhibitor candidates among natural compounds for the treatment
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EGFR Kinase Inhibiting Amino-enones for Breast Cancer; CADD Approach Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2024-02-01 Deena Gladies Raymond Mohanraj, Manikandan Alagumuthu, Subha Chellam, Abishek Suresh Kumar, Tejaswini Nagaraj Poojari, Jeevitha Suresh Kumar, Palaniraja Subramaniam
Background:: The Computer-Aided Drug Discovery (CADD) approach was used to develop a few Epidermal Growth Factor Receptor (EGFR) kinase inhibitors. EGFR kinase expression is highly associated with genomic instability, higher proliferation, lower hormone receptor levels, and HER2 over-expression. It is more common in breast cancer. Thus, EGFR Kinase is one of the main targets in discovering new cancer
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An In silico Study on B-cell Epitope Mapping of Acinetobacter baumannii Outer Membrane Protein K Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2024-01-29 Hana Heidarinia, Keyghobad Ghadiri, Fatemeh Nemati Zargaran, Roya Chegene Lorestani, Mosayeb Rostamian
Background: Acinetobacter baumannii is one of the main causes of nosocomial infections. No vaccine has yet been licensed for use in humans, and efforts are still ongoing. Objective: In the present study, we have predicted the B-cell epitopes of A. baumannii’s outer membrane protein K (OMPK) by using epitope prediction algorithms as possible vaccine candidates for future studies. Methods: The linear
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Designing Drug Delivery Vehicles based on N-(2-Hydroxypropyl) Methacrylamide Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2024-01-29 Ramakrishna Prasad Are, Anju R. Babu
Background: The development of polymeric-based drug delivery has seen faster growth in the past two decades. In polymers, copolymers as drug carriers are increasing to decrease the drug compounds' side effects and dosage-related toxicity. Objectives: The study's primary objective is to utilize computational resources to design drug molecules and perform in silco physicochemical property analysis. In
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Identification of Novel Marine Bioactive Compound as Potential Multiple Inhibitors in Triple-negative Breast Cancer - An in silico Approach Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2024-01-21 Hema Priya Manivannan, Vishnu Priya Veeraraghavan, Arul Prakash Francis
Background: Triple-negative breast cancer (TNBC) is a highly aggressive form of breast cancer lacking specific receptors, with dysregulated and overactivated Hedgehog (Hh) and mTOR/PI3K/AKT signaling pathways as potential therapeutic targets. Objective: This study aimed to identify potential inhibitors among 53 alkaloids derived from 9 marine bryozoans using in silico approaches. It sought to analyze
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Molecular Mechanism Analysis of the Effect of Hederagenin Combined with L-OHP on Chemosensitivity of AGS/L-OHP Based on Network Pharmacology Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2024-01-21 Hongyue Tang, Chao Wang, Chenhao Xing, Guoxin liang, Chang Guo, Xin Liu, YanJie Li, Mingming Zhang
Aims and Objectives: This study aimed to evaluate the pharmacological mechanism of Hederagenin (HD) combined with oxaliplatin (L-OHP) in treating gastric cancer (GC) through network pharmacology combined with experimental verification. background: Gastric cancer (GC) is the world’s most common gastrointestinal cancer[1]. This malignancy is of challenge to be eradicated by surgical operation since most
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Computational Study of Antimicrobial Peptides for Promising Therapeutic Applications Against Methicillin-resistant Staphylococcus aureus Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2024-01-17 Priyanka Sinoliya, Pooran Singh Solanki, Ravi Ranjan Kumar Niraj, Vinay Sharma
Background: Methicillin-resistant Staphylococcus aureus (MRSA) is a causative agent for multiple drug-resistant diseases and is a prime health concern. Currently, antibiotics like vancomycin, daptomycin, fluoroquinolones, linezolid, fifth-generation cephalosporin and others are available in the market for the treatment of MRSA infection. Methods: With the increasing prevalence of drug-resistant cases
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Exploration of Pharmacological Mechanisms of Dapagliflozin against Type 2 Diabetes Mellitus through PI3K-Akt Signaling Pathway based on Network Pharmacology Analysis and Deep Learning Technology Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2024-01-11 Jie Wu, Yufan Chen, Shuai Shi, Junru Liu, Fen Zhang, Xingxing Li, Xizhi Liu, Guoliang Hu, Yang Dong
Background:: Dapagliflozin is commonly used to treat type 2 diabetes mellitus (T2DM). However, research into the specific anti-T2DM mechanisms of dapagliflozin remains scarce. Objective:: This study aimed to explore the underlying mechanisms of dapagliflozin against T2DM. Methods:: Dapagliflozin-associated targets were acquired from CTD, SwissTargetPrediction, and SuperPred. T2DM-associated targets
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In-silico Design, ADMET Screening, Prime MM-GBSA Binding Free Energy Calculation and MD Simulation of Some Novel Phenothiazines as 5HT6R Antagonists Targeting Alzheimer’s Disease Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2024-01-11 PREMA V, Meena A, Ramalakshmi N
Background: Alzheimer's disease is a type of dementia that affects neuronal function, leading to a decline in cognitive functions. Serotonin-6 (5HT6) receptors are implicated in the etiology of neurological diseases. 5HT6 receptor antagonists act as anti-dementia agents. PDB ID: 7YS6 represents a membrane protein, and amplification and overexpression of this protein are associated with Alzheimer's
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PyComp: A Versatile Tool for Efficient Data Extraction, Conversion, and Management in High-throughput Virtual Drug Screening Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2024-01-09 Mohsen Sisakht, Mohammad Keyvanloo Shahrestanaki, Jafar Fallahi, Vahid Razban
Background: Virtual screening (VS) is essential for analyzing potential drug candidates in drug discovery. Often, this involves the conversion of large volumes of compound data into specific formats suitable for computational analysis. Managing and processing this wealth of information, especially when dealing with vast numbers of compounds in various forms, such as names, identifiers, or SMILES strings
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Discovery of Novel Pyrimidine Based Small Molecule Inhibitors as VEGFR-2 Inhibitors: Design, Synthesis, and Anti-Cancer Studies Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2024-01-08 Sachin A. Dhawale, Santosh N. Mokale, Pratap S. Dabhade
Background: Receptor tyrosine kinases (RTKs) are potent oncoproteins in cancer that, when mutated or overexpressed, can cause uncontrolled growth of cells, angiogenesis, and metastasis, making them significant targets for cancer treatment. Vascular endothelial growth factor receptor 2 (VEGFR2), is a tyrosine kinase receptor that is produced in endothelial cells and is the most crucial regulator of
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Network Pharmacology and Bioinformatics Analyses Identify the Core Genes and Pyroptosis-Related Mechanisms of Nardostachys Chinensis for Atrial Fibrillation Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2024-01-05 Weiqi Xue, Yuan Luo, Weifeng He, Mengyuan Yan, Huanyi Zhao, Lijin Qing
Background: Nardostachys chinensis is an herbal medicine widely used in the treatment of atrial fibrillation (AF), but the mechanism is unclear. Objective: To explore the molecular mechanism of N. chinensis against AF. objective: To explore molecular mechanism of NC against AF. Methods: The TCMSP was used to screen the active N. chinensis compounds and their targets. Differentially expressed genes
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In Silico Study on Natural Chemical Compounds from Citric Essential Oils as Potential Inhibitors of an Omicron (BA.1) SARS-CoV-2 Mutants’ Spike Glycoprotein Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2024-01-05 Olha Ovchynnykova, Jordhan D. Booth, Trey M. Cocroft, Kostyantyn M. Sukhyy, Karina Kapusta
Background: SARS-CoV-2's remarkable capacity for genetic mutation enables it to swiftly adapt to environmental changes, influencing critical attributes, such as antigenicity and transmissibility. Thus, multi-target inhibitors capable of effectively combating various viral mutants concurrently are of great interest. Objective: This study aimed to investigate natural compounds that could unitedly inhibit
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Identify Diabetes-related Targets based on ForgeNet_GPC Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2024-01-04 Bin Yang, Linlin Wang, Wenzheng Bao
Background:: Research on potential therapeutic targets and new mechanisms of action can greatly improve the efficiency of new drug development. Aims:: Polygenic genetic diseases, such as diabetes, are caused by the interaction of multiple gene loci and environmental factors. Objective:: In this study, a disease target identification algorithm based on protein recognition is proposed. Methods:: In this
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Integrated Bioinformatics Analysis and Target Drug Prediction of Inflammatory Bowel Disease Co-existent Diabetes Mellitus Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2024-01-04 Lili Yang, Ning Wang, Yutong Wang, Wen Li, Ziyang Kong, Bin Zhang, Yaoyao Bian
Introduction: Inflammatory bowel disease (IBD) has become one of the public problems worldwide and its incidence rate is increasing year by year. Its concomitant disease i.e. diabetes mellitus (DM) has attracted more and more attention due to DM altering the progression of IBD and leading to long periods of intermittent recurrence and deterioration. The common mechanism and potential target drug of
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Design, In Silico Screening, Synthesis, Characterisation and DFT-based Electronic Properties of Dihydropyridine-based Molecule as L-type Calcium Channel Blocker Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2023-12-27 Sujoy Karmakar, Hriday Kumar Basak, Uttam Paswan, Soumen Saha, Samir Kumar Mandal, Abhik Chatterjee
Objective: The objectives of this study are first to design potential antihypertensive drugs based on the DHP scaffold, secondly, to analyse drug-likeness properties of the ligands and investigate their molecular mechanisms of binding to the model protein Cav1.2 and finally to synthesise the best ligand. Methods: Due to the lack of 3D structures for human Cav1.2, the protein structure was modelled
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DeepTransformer: Node Classification Research of a Deep Graph Network on an Osteoporosis Graph based on GraphTransformer Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2023-12-01 Yixin Liu, Guowei Jiang, Miaomiao Sun, Ziyan Zhou, Pengchen Liang, Qing Chang
Background:: Osteoporosis (OP) is one of the most common diseases in the elderly population. It is mostly treated with medication, but drug research and development have the disadvantage of taking a long time and having a high cost. Objective:: Therefore, we developed a graph neural network with the help of artificial intelligence to provide new ideas for drug research and development for OP. Methods::
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Insights into the Molecular Mechanisms of Bushen Huoxue Decoction in Breast Cancer via Network Pharmacology and in vitro experiments Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2023-12-01 Hongyi Liang, Guoliang Yin, Guangxi Shi, Xiaofei Liu, Zhiyong Liu, Jingwei Li
Aim:: Breast cancer (BC) is by far seen as the most common malignancy globally, with 2.261 million patients newly diagnosed, accounting for 11.7% of all cancer patients, according to the Global Cancer Statistics Report (2020). The luminal A subtype accounts for at least half of all BC diagnoses. According to TCM theory, Bushen Huoxue Decoction (BSHXD) is a prescription used for cancer treatment that
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Mechanism of Polygala-Acorus in Treating Autism Spectrum Disorder Based on Network Pharmacology and Molecular Docking Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2023-12-01 Haozhi Chen, Changlin Zhou, Wen Li, Yaoyao Bian
Background:: 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. Polygala–Acorus, used as a pair drug, positively affects the brain and kidneys, and can improve intelligence, wisdom
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Clodronic Acid has Strong Inhibitory Interactions with the Urease Enzyme of Helicobacter Pylori: Computer-aided Design and in vitro Confirmation Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2023-11-14 Mohsen Karami Fath, Saeed Khalili, Masoud Mashhadi Akbar Boojar, Zahra Sadat Hashemi, Mahboubeh Zarei
Background: Helicobacter Pylori (HP) infection could lead to various gastrointestinal diseases. Urease is the most important virulence factor of HP. It protects the bacterium against gastric acid. Objective: Therefore, we aimed to design urease inhibitors as drugs against HP infection. Methods: The DrugBank-approved library was assigned with 3D conformations and the structure of the urease was prepared
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Computer-aided Design of Wide-spectrum Coronavirus Helicase NSP13 Cage Inhibitors: A Molecular Modelling Approach Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2023-11-06 Vadim Shiryaev, Yuri Klimochkin
Background:: The coronavirus helicase NSP13 plays a critical role in its life cycle. The found NSP13 inhibitors have been tested only in vitro but they definitely have the potential to become antiviral drugs. Thus, the search for NSP13 inhibitors is of great importance. background: The coronavirus helicase nsp13 plays a critical role in its life cycle. The found nsp13 inhibitors have been tested only
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Rational Design of Dual Inhibitors for Alzheimer's Disease: Insights from Computational Screening of BACE1 and GSK-3β Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2023-11-06 Magham Sai Varshini, Ramakkamma Aishwarya Reddy, Praveen T. Krishnamurthy, Divakar Selvaraj
Background:: Alzheimer's disease (AD) is one of the most concerned neurodegenerative disorders across the world characterized by amyloid-beta (Aβ) plaques and neurofibrillary tangles (NFTs), leading to cognitive decline and memory loss. Targeting key pathways involved in AD like Aβ and NFT pathways, are crucial for the development of effective therapeutic strategies. In this study, we aimed to identify
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A Novel Deep Learning Model for Drug-drug Interactions Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2023-11-03 Ali K. Abdul Raheem, Ban N. Dhannoon
Introduction: Drug-drug interactions (DDIs) can lead to adverse events and compromised treatment efficacy that emphasize the need for accurate prediction and understanding of these interactions. Methods: in this paper, we propose a novel approach for DDI prediction using two separate message-passing neural network (MPNN) models, each focused on one drug in a pair. By capturing the unique characteristics
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In-silico Assessment of Polyherbal Oils as Anti-diabetic Therapeutics Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2023-10-23 Amul S. Bahl, Vipin Kumar Verma, Vaishali Prajapati, Jagriti Bhatia, Dharamvir Singh Arya
Background: Diabetes mellitus (DM) is characterized by elevated blood glucose levels either due to insufficient insulin production, defective insulin action, or both. It affects nearly 537 million individuals worldwide. Pharmacological treatment involves the use of oral antidiabetic agents as mono or combination therapy that effectively aids in controlling hyperglycemia. Despite providing therapeutic
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Exploring the Molecular Mechanism of Niuxi-Mugua Formula in Treating Coronavirus Disease 2019 via Network Pharmacology, Computational Biology, and Surface Plasmon Resonance Verification Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2023-10-19 Wei Wang, Xu Cao, Yi-nan Cao, Lian-lian Liu, Shu-ling Zhang, Wen-ying Qi, Jia-xin Zhang, Xian-zhao Yang, Xiao-ke Li, Xiao-bin Zao, Yong-an Ye
Background: In China, Niuxi-Mugua formula (NMF) has been widely used to prevent and treat coronavirus disease 2019 (COVID-19). However, the mechanism of NMF for treating COVID-19 is not yet fully understood. Objective: This study aimed to explore the potential mechanism of NMF for treating COVID-19 by network pharmacology, computational biology, and surface plasmon resonance (SPR) verification. Methods:
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Fluorinated Diaryl Sulfonamides: Molecular Modeling, Synthesis, and In Vitro Validation as New CETP Inhibitors Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2023-10-18 Reema Abu Khalaf, Azhar Shalluf, Maha Habash
Background: Hyperlipidemia, a cardiovascular disease risk factor, is characterized by a rise in low-density lipoprotein (LDL), triglycerides and total cholesterol, and a decrease in high-density lipoprotein (HDL). Cholesteryl ester transfer protein (CETP) enables the transfer of cholesteryl ester from HDL to LDL and very low-density lipoprotein. Objective: CETP inhibition is a promising approach to
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Optimizing the Extraction of Polyphenols from the Bark of Terminalia arjuna and an In-silico Investigation on its Activity in Colorectal Cancer Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2023-10-17 Tathagata Adhikary, Piyali Basak
Background: The interconnection between different fields of research has gained interest due to its cutting-edge perspectives in solving scientific problems. Terminalia arjuna is indigenously used in India for curing several diseases, and its pharmacological activities are being revisited in recent drug-repurposing research. Objectives: Efficient ultrasound-assisted extraction of phytochemicals from
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Molecular Modelling of Resveratrol Derivatives with SIRT1 for the Stimulation of Deacetylase Activity Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2023-10-12 Mozhdeh Zamani, Pooneh Mokarram, Mehdi Jamshidi, Morvarid Siri, Hadi Ghasemi
Background: Resveratrol is a polyphenol that is found in plants and has been proposed to have a potential therapeutic effect through the activation of SIRT1, which is a crucial member of the mammalian NAD+ -dependent deacetylases. However, how its activity is enhanced toward specific substrates by resveratrol derivatives has not been studied. This study aimed to evaluate the types of interaction of
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Identification of Prognostic Markers and Potential Therapeutic Targets using Gene Expression Profiling and Simulation Studies in Pancreatic Cancer Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2023-10-12 Samvedna Singh, Aman Chandra Kaushik, Himanshi Gupta, Divya Jhinjharia, Shakti Sahi
Background: Pancreatic ductal adenocarcinoma (PDAC) has a 5-year relative survival rate of less than 10% making it one of the most fatal cancers. A lack of early measures of prognosis, challenges in molecular targeted therapy, ineffective adjuvant chemotherapy, and strong resistance to chemotherapy cumulatively make pancreatic cancer challenging to manage. Objective: The present study aims to enhance
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In-Silico Investigation of Ginseng Phytoconstituents as Novel Therapeutics Against MAO-A Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2023-10-11 Diksha Choudhary, Rajwinder Kaur, Nidhi Rani, Thakur Gurjeet Singh, Bhupinder Kumar
Background: Ginseng (Panax ginseng) is a herb of medicinal and nutritional importance. Ginseng has been used since ancient times for the treatment of numerous ailments as it has many therapeutic properties. Several phytoconstituents are present in Panax ginseng that possess a variety of beneficial pharmacological properties. Objective: To explore the potential of phytoconstituents of Panax ginseng
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Synthesis, and In-silico Studies of Indole-chalcone Derivatives Targeting Estrogen Receptor Alpha (ER-α) for Breast Cancer Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2023-10-04 Rahul Charudatta Choudhari, Kamalpreet Kaur, Agnidipta Das, Vikas Jaitak
Background: Breast cancer is the prominent reason of death in women worldwide, and the cases are increasing day by day. There are many FDA-approved drugs for treating breast cancer. Due to drug resistance, and problems in selectivity, there is a need to develop more effective agents with few side effects. Indole derivatives have demonstrated significant pharmacological potential as anti-breast cancer
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Network Pharmacology, Molecular Docking and Experimental Verification Revealing the Mechanism of Fule Cream against Childhood Atopic Dermatitis Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2023-10-02 Chang Liu, Yuxin Liu, Yi Liu, Jing Guan, Ying Gao, Ling Ou, Yuenan Qi, Xiaoxi Lv, Jianmin Zhang
Background: The Fule Cream (FLC) is an herbal formula widely used for the treatment of pediatric atopic dermatitis (AD), however, the main active components and functional mechanisms of FLC remain unclear. This study performed an initial exploration of the potential acting mechanisms of FLC in childhood AD treatment through analyses of an AD mouse model using network pharmacology, molecular docking
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Automation of Drug Discovery through Cutting-edge In-silico Research in Pharmaceuticals: Challenges and Future Scope Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2023-10-02 Smita Singh, Pranjal Kumar Singh, Kapil Sachan, Mukesh Kumar, Poonam Bhardwaj
The rapidity and high-throughput nature of in silico technologies make them advantageous for predicting the properties of a large array of substances. In silico approaches can be used for compounds intended for synthesis at the beginning of drug development when there is either no or very little compound available. In silico approaches can be used for impurities or degradation products. Quantifying
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Efficacy and Safety of PARP Inhibitor Therapy in Advanced Ovarian Cancer: A Systematic Review and Network Meta-analysis of Randomized Controlled Trials Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2023-09-20 Juying Chen, Xiaozhe Wu, Hongzhe Wang, Xiaoshan Lian, Bing Li, Xiangbo Zhan
Aims: This study aims to evaluate the efficacy and safety of PARP inhibitor therapy in advanced ovarian cancer and identify the optimal treatment for the survival of patients. Background: The diversity of PARP inhibitors makes clinicians confused about the optimal strategy and the most effective BRCAm mutation-based regimen for the survival of patients with advanced ovarian cancer. Objectives: The
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Hibiscus sabdariffa Linn. Extract Increases the mRNA Expression of the Arcuate Nucleus Leptin Receptor and is Predicted in silico as an Anti-obesity Agent Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2023-09-19 Neng Tine Kartinah, Suci Anggraini, Fadilah Fadilah, Rickie Rickie
Background: Leptin is predominant in regulating body weight by stimulating energy expenditure through its neuronal action in the brain. Moreover, it is projected to adipose tissue and induces adipocyte browning by activating the β3-adrenergic receptor (β3AR). However, the expression of leptin receptor (Lep-R) and β3AR in people with obesity is downregulated. Aim: We hypothesized that Hibiscus sabdariffa
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Advances in Drug Discovery and Design Using Computer-Aided Molecular Modeling Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2023-09-14 Kuldeep Singh, Bharat Bhushan, Bhoopendra Singh
: Computer-aided molecular modeling is a rapidly emerging technology that is being used to accelerate the discovery and design of new drug therapies. It involves the use of computer algorithms and 3D structures of molecules to predict interactions between molecules and their behavior in the body. This has drastically improved the speed and accuracy of drug discovery and design. Additionally, computer-aided
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A Computational Approach for Designing and Validating Small Interfering RNA against SARS-CoV-2 Variants Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2023-09-14 Kishore Dhotre, Debashree Dass, Anwesha Banerjee, Vijay Nema, Anupam Mukherjee
Aims: The aim of this study is to develop a novel antiviral strategy capable of efficiently targeting a broad set of SARS-CoV-2 variants. Background: Since the first emergence of SARS-CoV-2, it has rapidly transformed into a global pandemic, posing an unprecedented threat to public health. SARS-CoV-2 is prone to mutation The study contributes to the possibility of designing and developing an effective
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Machine Learning Algorithms Identify Target Genes and Molecular Mechanism of Matrine against Diffuse Large B-cell Lymphoma Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2023-09-14 Yidong Zhu, Zhongping Ning, Ximing Li, Zhikang Lin
Background: Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin's lymphoma worldwide. Novel treatment strategies are still needed for this disease. Objective: The present study aimed to systematically explore the potential targets and molecular mechanisms of matrine in the treatment of DLBCL. Methods: Potential matrine targets were collected from multiple platforms. Microarray
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To Explore the Mechanism of Maiwei Dihuang Decoction in the Treatment of Non-small Cell Lung Cancer based on Network Pharmacology Combined with LC-MS Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2023-09-13 Tao Jiang, Yang Lu, Wanzhi Yang, Jinhong Xu, Mingxing Zhu, Yong Huang, Fang Bao, Shengqi Zheng, Yongxia Li
Objective: To explore the mechanism of Maiwei Dihuang decoction in the treatment of non-small cell lung cancer (NSCLC) by using network pharmacology and LC-MS technology. Methods: The effective components in Maiwei Dihuang decoction were detected by liquid chromatography- mass spectrometry (LC-MS). Use the SuperPred database to collect the relevant targets of the active ingredients of Mai Wei Di Tang
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Banxia Xiexin Decoction Prevents HT22 Cells from High Glucose-induced Neurotoxicity via JNK/SIRT1/Foxo3a Signaling Pathway Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2023-09-13 Yinli Shi, Pei Sheng, Ming Guo, Kai Chen, Yun Zhao, Xu Wang, Mianhua Wu, Bo Li
Background: Type 2 diabetes-associated cognitive dysfunction (DCD) is a chronic complication of diabetes that has gained international attention. The medicinal compound Banxia Xiexin Decoction (BXXXD) from traditional Chinese medicine (TCM) has shown potential in improving insulin resistance, regulating endoplasmic reticulum stress (ERS), and inhibiting cell apoptosis through various pathways. However
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Chemical Composition, In vitro and In silico Evaluation of Essential Oil from Ocimum tenuiflorum and Coriandrum sativum Linn for Lung Cancer Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2023-09-11 Bhim Singh, Kumari Sunita Prajapati, Amit Kumar, Shivam Patel, Shashank Kumar, Vikas Jaitak
Background: Medicinal plants play an essential role in everyday life; plants highly contain therapeutic phytoconstituents commonly used to treat various diseases. This paper discusses the Chemical composition, In vitro antiproliferative activity and In silico study of essential oil extracted from Ocimum tenuiflorum (family Lamiaceae) and Coriandrum sativum (family Apiaceae). Objective: In present study
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Unearthing Insights into Metabolic Syndrome by Linking Drugs, Targets, and Gene Expressions Using Similarity Measures and Graph Theory Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2023-09-06 Alwaz Zafar, Bilal Wajid, Ans Shabbir, Fahim Gohar Awan, Momina Ahsan, Sarfraz Ahmad, Imran Wajid, Faria Anwar, Fazeelat Mazhar
Aims and Objectives:Metabolic syndrome (MetS) is a group of metabolic disorders that includes obesity in combination with at least any two of the following conditions, i.e., insulin resistance, high blood pressure, low HDL cholesterol, and high triglycerides level. Treatment of this syndrome is challenging because of the multiple interlinked factors that lead to increased risks of type-2 diabetes and
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The Potential Roles of Ficus carica Extract in the Management of COVID-19 Viral Infections: A Computer-aided Drug Design Study Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2023-09-04 Mahmoud Hamed, Maha Khalifa, Mahmoud A. El Hassab, Mohammed A. S. Abourehab, Omkulthom Al kamaly, Ashwag S. Alanazi, Wagdy M. Eldehna, Fotouh R. Mansour
Introduction: The conventional processes of drug discovery are too expensive, timeconsuming and the success rate is limited. Searching for alternatives that have evident safety and potential efficacy could save money, time and improve the current therapeutic regimen outcomes. Methods: Clinical phytotherapy implies the use of extracts of natural origin for prophylaxis, treatment, or management of human
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The Diagnostic Features of Peripheral Blood Biomarkers in Identifying Osteoarthritis Individuals: Machine Learning Strategies and Clinical Evidence Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2023-08-31 Qiao Zhou, Jian Liu, Ling Xin, Yuedi Hu, Yajun Qi
Background: People with osteoarthritis place a huge burden on society. Early diagnosis is essential to prevent disease progression and to select the best treatment strategy more effectively. In this study, the aim was to examine the diagnostic features and clinical value of peripheral blood biomarkers for osteoarthritis. Objective: The goal of this project was to investigate the diagnostic features
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Molecular Docking and Molecular Dynamics Simulation of New Potential JAK3 Inhibitors Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2023-08-30 Qidi Zhong, Jiarui Qin, Kaihui Zhao, Lihong Guo, Dongmei Li
Introduction: JAK3 kinase inhibitor has become an effective means to treat tumors and autoimmune diseases. Methods: In this study, molecular docking and molecular dynamics simulation were used to study the theoretical interaction mechanism between 1-phenylimidazolidine-2-one molecules and JAK3 protein. Results: The results of molecular docking showed that the six 1-phenylimidazolidine-2-one derivatives
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Unveiling the Anti-convulsant Potential of Novel Series of 1,2,4-Triazine- 6H-Indolo[2,3-b]quinoline Derivatives: In Silico Molecular Docking, ADMET, DFT, and Molecular Dynamics Exploration Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2023-08-28 Hariram Singh, Devender Pathak
Background: Epilepsy is a chronic neurological disorder caused by irregular electrical activity in the brain. To manage this disorder effectively, it is imperative to identify potential pharmacological targets and to understand the pathophysiology of epilepsy in depth. Objective: This research aimed to identify promising leads from a library of 1,2,4-triazine-6Hindolo[ 2,3-b]quinoline derivatives and
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Investigation of Iminosugars as Antiviral Agents against SARS-CoV-2 Main Protease: Inhibitor Design and Optimization, Molecular Docking, and Molecular Dynamics Studies to Explore Potential Inhibitory Effect of 1-Deoxynojirmycin Series Curr. Comput.-Aided Drug Des. (IF 1.7) Pub Date : 2023-08-23 Vashima Miglani, Parul Sharma, Anudeep Kumar Narula
Background: The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) poses an enormous challenge to human health and economy at a global level. According to WHO's latest data, till now, there have been a total of 641,435,884 confirmed cases of COVID-19, and the associated deaths are 6,621,060. Though few vaccinations have been approved for emergency usage, antiviral medications for long-term