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In silico screening of selective ATP mimicking inhibitors targeting the Plasmodium falciparum Grp94 J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-18 Melissa Louise Stofberg, Florence Lisa Muzenda, Ikechukwu Achilonu, Erick Strauss, Tawanda Zininga
Plasmodium falciparum parasites export more than 400 proteins to remodel the host cell environment and increase its chances of surviving and reproducing. The endoplasmic reticulum (ER) plays a cent...
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Computational choreography: dissecting the dance of hydrogen bonding and π–π stacking in the fluorescence discrimination mechanism of ciprofloxacin with supramolecular assembly J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-18 Jaymin Parikh, Keyur Bhatt, Krunal Modi, Ajay Desai, Nihal Patel, Chirag Patel, Ravibhai Bhola
The detailed binding insight between the fluorophore and analyte plays a pivotal role in the design of an efficient chemosensor for water pollution. In this study, we designed a picolinic acid-func...
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Unraveling the ligand specificity and promiscuity of the Staphylococcus aureus NorA efflux pump: a computational study J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-18 Esra Büşra Işık, Onur Serçinoğlu
Staphylococcus aureus, a gram-positive bacterial pathogen, develops antibiotic resistance partly through enhanced activity of transmembrane multi-drug efflux pump proteins like NorA. Being a promin...
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Synergistic inhibition mechanism of quinazolinone and piperacillin on penicillin-binding protein 2a: a promising approach for combating methicillin-resistant Staphylococcus aureus J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-18 Fangfang Jiao, Weirong Cui, Pinkai Wang, Henry H. Y. Tong, Jingjing Guo, Jun Tao
The production of penicillin-binding protein 2a (PBP2a), a cell wall synthesis protein, is primarily responsible for the high-level resistance observed in methicillin-resistant Staphylococcus aureu...
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Potential diagnostic value of serum microRNAs for 19 cancer types: a meta-analysis of bioinformatics data J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-15 ChauMyThanh Tran, PhongSon Dinh
Cancer is the second most common cause of mortality worldwide, accounting for almost 10 million deaths in 2020. These deaths were partly due to delayed diagnosis that led to deferred treatment. The...
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Synthesis, spectroscopic analysis, and computational-based investigations on ‘azo-coumarin-Co(II)-galangin’ hybrids exhibit multipotential activities J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-14 Shasank Sekhar Swain, Alaka Sahoo, Satya Ranjan Singh, Jyotirmaya Sahoo, Sudhir Kumar Paidesetty
The present study synthesized a series of cobalt (II) metal ion frame hybrid candidates (6a–6f) bearing phyto-flavonol galangin with substituted aryl diazenyl coumarins, and further structural conf...
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A quinoxaline-based derivative exhibited potent and selective anticancer activity with apoptosis induction in PC-3 cells through Topo II inhibition J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-14 Mayada E. G. Elsakka, Mohamed M. Tawfik, Lamiaa A. A. Barakat, Mohamed S. Nafie
Quinoxaline constitutes a variety of derivatives that exhibit a range of biological characteristics, including anti-inflammatory and antitumor effects, and their importance in therapeutic chemistry...
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Amino acids and glycine derivatives differently affect refolding of mesophilic and thermophilic like α-amylases: implications in protein refolding and aggregation J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-14 Aziz Ahmad, Prachi Joshi, Rajesh Mishra
α-amylases are industrially important enzymes which are used in different starch-based industries. They are adapted to different environmental conditions like extremes of temperature, pH and salini...
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Whole proteome screening to develop a potent epitope-based vaccine against Coxiella burnetii: a reverse vaccinology approach J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-15 Ali Forouharmehr
Coxiellosis is known as a threat to human health. This study aimed to develop an epitope-based vaccine against coxiellosis using a whole proteome investigation. In this case, the whole proteome of ...
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Mechanistic insights into interactions between ionizable lipid nanodroplets and biomembranes J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-15 Petra Čechová, Markéta Paloncýová, Martin Šrejber, Michal Otyepka
Delivery of RNA into cells using lipid nanoparticles (LNPs) has been a significant breakthrough in RNA-based medicine, with clinical applicability expanded through the use of ionizable lipids (ILs)...
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A novel immunoinformatics approach for developing a poly-epitope vaccine targeting foot and mouth disease virus, exploiting structural VP proteins J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-15 Muhammad Saad Bhutta, Muhammad Awais, Sahar Sadaqat, Fernando Berton Zanchi, Naila Shahid, Abdul Qayyum Rao
Foot and mouth Disease virus (FMDV) belongs to Picornaviridae family and Aphthovirus genus causing Foot and mouth disease (FMD) in cloven-hoofed animals. FMDV, a prevalent virus induces both acute ...
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Network-base approaches to identify therapeutic biomarkers in hepatocellular carcinoma and search for drug hunting utilizing molecular dynamics simulations J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-14 Hassan Ayaz, Faisal Ahmad, Sajjad Ahmad, Qaiser Arfan, Abdullah F. Alasmari, Farhan Siddique, Bushra Rehman, Adnan Zeb, Sergio Crovella, Syed Shujait Ali, Yasir Waheed, Muhammad Suleman
The presence of conditions like Alpha-1 antitrypsin deficiency, hemochromatosis, non-alcoholic fatty liver diseases and metabolic syndrome can elevate the susceptibility to hepatic cellular carcino...
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In silico strategies for identifying therapeutic candidates against Acinetobacter baumannii: spotlight on the UDP-N-acetylmuramoyl-L-alanine-D-glutamate:meso-diaminopimelate ligase (MurE) J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-14 Ankit Kumar, Pratyaksha Singh, Ekampreet Singh, Monika Jain, Jayaraman Muthukumaran, Amit Kumar Singh
The opportunistic bacterium Acinetobacter baumannii, which belongs to ESKAPE group of pathogenic bacteria, is leading cause of infections associated with gram-negative bacteria. Acinetobacter bauma...
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Zingiberaceae-derived phytomolecules inhibit Japanese encephalitis virus RNA dependent RNA polymerase: a molecular dynamics study J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-14 Aftab Alam, Asma Anjum, Ehssan H. Moglad, Talha Jawaid, Ahmed I. Foudah, Faisal Alotaibi, Faris F. Aba Alkhayl, Mohammad Azhar Kamal, Mohiuddin Khan Warsi, Mohamed F. Balaha
The Japanese encephalitis virus, (JEV), is a flavivirus mostly transmitted by Culex mosquitoes mostly present in Southeast Asia and the Western Pacific region. Ardeid-wading birds are the natural r...
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Multistate B- to A- transition in protein-DNA Binding – How well is it described by current AMBER force fields? J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-14 Petr Jurečka, Marie Zgarbová, Filip Černý, Jan Salomon
When DNA interacts with a protein, its structure often undergoes a significant conformational adaptation, usually involving a transition from B-DNA towards the A-DNA form. This is not a two-state, ...
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Structural insights into non-hotspot KRAS mutations and their potential as targets for effective cancer therapies J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-14 Cong Ding, Gaoyuan Wang, Wenqing Zou, Yanping Mao, Jun Ma
Kirsten rat sarcoma virus protein (KRAS) is a protein that plays a central role in signal transduction using extracellular signal regulated kinase (ERK) and mitogen activated protein kinase (MAPK) ...
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Molecular interaction of quercetin and its derivatives against nucleolin in breast cancer: in-silico and in-vitro study J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-11 Siuli Shaw, Mukesh Chourasia, Ranu Nayak, Tushar Kumeria, Madhumita P. Ghosh, Seneha Santoshi, Sudeep Bose
Nucleolin, a multifaceted RNA binding domain protein is overexpressed in various cancers leading to dysfunction of several cellular signaling pathways. Quercetin, a distinctive bioactive molecule, ...
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A new trivalent recombinant protein for type 2 diabetes mellitus with oral delivery potential: design, expression, and experimental validation J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-11 Maryam Ehsasatvatan, Bahram Baghban Kohnehrouz
Glucagon-like peptide-1 (GLP-1) receptor agonists are increasingly used in clinical practice for the management of type 2 diabetes mellitus. However, the extremely short half-life of GLP-1 and the ...
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Multiomics-based classifier to decipher immune landscape of uveal melanoma and predict patient outcomes J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-11 Yuan Zhang, Ni Shen, Aimin Jiang, Jiawei Zhao, Yanzhi Sang, Anbang Wang, Wei Shen, Yu Gao
Uveal melanoma (UVM) prognosis and the possibilities for targeted therapy depend on a thorough understanding of immune infiltration features and the analysis of genomic and immune signatures. Lever...
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In-silico analysis of potential anticancer drug for NEK7 and PPP1CA proteins overexpressed in pancreatic ductal adenocarcinoma J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-12 Safa Adrees, Anam Imtiaz, Aiman Yaseen, Muhammad Irfan Fareed, Waqar Anwar, Asma Ashraf, Rana Muhammad Kamran Shabbir, Shaista Andlib, Mureed Hussain, Asma Tariq, Rana Muhammad Mateen, Muhammad Arif Nadeem Saqib, Rukhsana Parveen
NIMA-related kinase 7 (NEK7) and phosphoprotein phosphatase-1 catalytic subunit alpha (PPP1CA) are the most common proteins overexpressed in pancreatic ductal adenocarcinoma, which is the most comm...
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Machine learning-based virtual screening and molecular modelling studies for identification of butyrylcholinesterase inhibitors as anti-Alzheimer’s agent J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-11 Ankit Ganeshpurkar, Likhit Akotkar, Devendra Kumar, Dileep Kumar, Aditya Ganeshpurkar
Butyrylcholinesterase (BChE) is a hydrolase involved in the metabolism and detoxification of specific esters in the blood. It is also implicated in the progression of Alzheimer’s disease, a type of...
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Guideline directed medical therapy induced nephrotoxicity in HFrEF patients; an insight to its mechanism J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-11 Anu Philip, Prarambh S. R. Dwivedi, C. S. Shastry, Basavaraj Utagi
Guideline Directed Medical Therapy (GDMT) has been the standard pharmacotherapy for the treatment of Heart Failure patients with reduced Ejection Fraction (HFrEF) recommended by the European Societ...
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The effect of phosphorylation on the conformational dynamics and allostery of the association of death-associated protein kinase with calmodulin J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-08 Xiaolong Li, Canglong Hou, Mingyuan Yang, Beier Luo, Ningfang Mao, Kai Chen, Ziqiang Chen, Yushu Bai
Protein phosphorylation plays an important role in the signal transduction and is capable of regulation of cell activity. The death-associated protein kinase 1 (DAPK1), as a Ser/Thr kinase, interac...
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Potential bioactive compound and hub gene identification of endometrial carcinoma using systems biology J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-09 Shanmugapriya Rishikesan, Parthiban Brindhadevi, Rajakumari K., N. Srinath, M. Balamugundhan
Endometrial carcinoma is a frequent cancer of the female genital tract. Endometrial carcinoma accounts for 97% of all uterine malignancies and 3 % of sarcomas that develop from the endometrium’s gl...
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Sakuranetin ameliorates streptozotocin-induced diabetes in rodents by inhibiting caspase-3 activity, modulating hematological parameters, and suppressing inflammatory cytokines: a molecular docking and dynamics study J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-09 Hassan H. Almasoudi, Mohammed H. Nahari, Abdulkarim S. Binshaya, Mohammed Ageeli Hakami, Abdulfattah Y. Alhazmi, Humood Al Shmrany, Abdullah Alqasem, Farhan R. Khan
Diabetes affects people of all ages, regardless of gender and background. To date, there is no evidence for the effect of sakuranetin against the streptozotocin (STZ)-induced diabetes paradigm. The...
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A network pharmacological approach for the identification of potential therapeutic targets of Brahmi Nei – a complex traditional Siddha formulation J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-09 Agnes Preethy H., Yanamandram Balasubramanian Venkatakrishnan, Vigneshwar Ramakrishnan, Uma Maheswari Krishnan
Brahmi Nei (BN), a traditional Indian polyherbal formulation has been described in classical texts for the treatment of anxiety and depression, as well as to fortify the immune system. The individu...
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Distinct characteristics of putative archaeal 5-methylcytosine RNA methyltransferases unveil their substrate specificities and evolutionary ancestries J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-07 Sayan Saha, Suraj Kumar Mandal, Shankar Prasad Kanaujia
5-Methylcytosine methyltransferases (m5C MTases) are known to be involved in the modification of RNA. Although these enzymes have been relatively well characterized in bacteria and eukarya, a compl...
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Exploration of novel hydroxamate zinc binding group inhibitors against HDAC-1-3 enzymes by AI-based virtual screening: atomistic insights from steered molecular dynamics J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-08 S. M. Esther Rubavathy, V. Rajapandian, M. Prakash
Overexpression of histone deacetylase (HDAC) enzymes is linked to a wide variety of illnesses, including malignancies and neurological disorders, which makes HDAC inhibitors potentially therapeutic...
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Identification of a novel drug molecule for neurodegenerative disease from marine algae through in-silico analysis J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-08 Anantha Krishnan Dhanabalan, Praveen Kumar, Saranya Vasudevan, Arkadiusz Chworos, Devadasan Velmurugan
Cognitive functions are lost due to the rapid hydrolysis of acetylcholine including Acetylcholinesterase (AChE) and Butyrylcholinesterase (BChE). Marine algae-derived compounds were reported for th...
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Cytotoxic monastrol derivatives as adjective inhibitors of drug-resistant Eg5: a molecular dynamics perspective J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-07 S. Shahabipour, A. N. Shamkhali, N. Razzaghi-Asl
The mitotic kinesin Eg5 is a motor protein involved in the formation of bipolar spindle and cell division. Eg5 is overexpressed in various cancer cells and Eg5 targeting agents are promising candid...
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In silico development of a novel anti-mutation, multi-epitope mRNA vaccine against MPXV variants of emerging lineage and sub-lineages by using immunoinformatics approaches J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-07 Caixia Tan, Jingxiang Zhou, Anhua Wu, Chunhui Li
Over the past year, an unexpected surge in human monkeypox (hMPX) cases has been observed. This outbreak differs from previous ones, displaying distinct epidemiological characteristics and transmis...
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Deep-VEGF: deep stacked ensemble model for prediction of vascular endothelial growth factor by concatenating gated recurrent unit with two-dimensional convolutional neural network J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-07 Raed Alsini, Abdullah Almuhaimeed, Farman Ali, Majdi Khalid, Majed Farrash, Atef Masmoudi
Vascular endothelial growth factor (VEGF) is involved in the development and progression of various diseases, including cancer, diabetic retinopathy, macular degeneration and arthritis. Understandi...
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In silico design, synthesis and antitubercular activity of novel 2-acylhydrazono-5-arylmethylene-4-thiazolidinones as enoyl-acyl carrier protein reductase inhibitors J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-07 Serap İpek Dingiş Birgül, Jyothi Kumari, Rasoul Tamhaev, Lionel Mourey, Christian Lherbet, Dharmarajan Sriram, Atilla Akdemir, İlkay Küçükgüzel
Mycobacteria regulate the synthesis of mycolic acid through the fatty acid synthase system type 1 (FAS I) and the fatty acid synthase system type-2 (FAS-II). Because mammalian cells exclusively uti...
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Molecular insights into ferric-siderophore transport by the putative TonB-dependent transporter in Mycobacterium tuberculosis J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-05 Gauri Shankar, Yusuf Akhter
Iron acquisition is critical to the virulence of Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis. To acquire iron within the host, Mtb secretes siderophores that chelate iron ...
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In vitro bioactivities and in silico enzyme interactions of abietatrien-3β-ol by bio-guided isolation from Nepeta italica subsp. italica J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-05 Yaşar İpek, Yunus Başar, Semiha Yenigün, Lütfi Behçet, Tevfik Özen, İbrahim Demirtaş
Abietatrien-3β-ol (ATO) was isolated from the aerial part of the Nepeta italica subsp. italica methanol-chloroform extract and studied antioxidant, enzyme inhibition, and DNA protection activities....
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Repurposing of SARS-CoV-2 compounds against Marburg Virus using MD simulation, mm/GBSA, PCA analysis, and free energy landscape J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-07 Sanjay Kumar, Rajni Dubey, Richa Mishra, Saurabh Gupta, Vivek Dhar Dwivedi, Subhasree Ray, Niraj Kumar Jha, Devvret Verma, Lung-Wen Tsai, Navneet Kumar Dubey
The significant mortality rate associated with Marburg virus infection made it the greatest hazard among infectious diseases. Drug repurposing using in silico methods has been crucial in identifyin...
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G-ACP: a machine learning approach to the prediction of therapeutic peptides for gastric cancer J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-07 Humera Azad, Muhammad Yasir Akbar, Jawad Sarfraz, Waseem Haider, Muhammad Naeem Riaz, Ghulam Muhammad Ali, Shakira Ghazanfar
Conventional Gastrointestinal (GI) cancer treatments are quite expensive and have major hazards. Nowadays, a different strategy places more emphasis on creating tiny biologically active peptides th...
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Immunomodulatory and anticytokine therapeutic potential of three Indian spices constituents and its hyaluronic acid conjugates for prevention and post COVID-19 complications: a computational modeling approach J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-06 P. Nandu Baby
Targeted drug delivery to SARS-CoV-2 host target proteins for preventing or blocking COVID-19 infection is making serious concern during COVID-19 pandemic and its consequent waves around the globe....
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Molecular modeling of novel 2-aminopyridine derivatives as potential JAK2 inhibitors: a rational strategy for promising anticancer agents J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-06 Nadia Munir, Tahir Ali Chohan, Aisha Qayyum, Talha Ali Chohan, Fakhra Batool, Mian Waqar Mustafa, Sirajudheen Anwar, Fawaz Alheibshy, Weiam Hussein, Ahmed Alafnan, Umair Khurshid, Anjum Khursheed, Hammad Saleem
Janus kinase 2(JAK2) is a potential target for anticancer drugs in the treatment of numerous myeloproliferative diseases due to its central role in the JAK/STAT signaling cascade. In this study, th...
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In silico analysis of small molecule compounds based on pharmacophore- and backbone-leaping peroxiredoxin 1 (PRDX1) inhibitors J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-06 Ningying Zheng, Huiting Tan, Tianli Lai, Zunnan Huang, Lianxiang Luo
Abnormal expression of PRDX has been found to play a significant role in the growth of colorectal cancer and other types of tumors. Despite the identification of several PRDX1 inhibitory compounds ...
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Computational study of the mechanism of binding of antifungal icofungipen in the active site of eukaryotic isoleucyl tRNA synthetase from Candida albicans J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-06 Shilpi Chowdhury, Nilashis Nandi
The eukaryotic fungal species Candida albicans is a critical infective pathogenic agent. The β-amino acid, Icofungipen, is an effective inhibitor of Candida albicans. Icofungipen binds at the activ...
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Salp-J Colony Optimization-based advanced hybrid ensemble deep predictor with LSTM for protein structure prediction J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-06 Swati Jadhav, Arati J. Vyavahare, Manish Sharma
Protein structure prediction (PSP) is a key concern in computational biology, which is considered a challenging task that is vital to determine the structure and the protein function since each pro...
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Antiviral actions of natural compounds against dengue virus RNA dependent RNA polymerase: insights from molecular dynamics and Gibbs free energy landscape J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-05 Ali A. Rabaan, Nawal A. Al Kaabi, Muzaheed, Mubarak Alfaresi, Mohammed Garout, Nouf Alotaibi, Ameen S. S. Alwashmi, Ahmed Alsayyah, Neda A. Alali, Tarek Sulaiman, Jawaher Alotaibi, Mohammed Alissa
Dengue fever, a major global health challenge, affects nearly half the world’s population and lacks effective treatments or vaccines. Addressing this, our study focused on natural compounds that po...
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Biochemical and computational inhibition of α-glucosidase by novel metronidazole-linked 1H-1,2,3-triazole and carboxylate moieties: kinetics and dynamic investigations J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-03 Saeed Ullah, Sobia Ahsan Halim, Muhammad Waqas, Farheen Mansoor, Satya Kumar Avula, Farhan A. Khan, Muhammad Perviaz, Hanan A. Ogaly, Ajmal Khan, Ahmed Al-Harrasi
In the current study, metronidazole derivatives containing 1H-1,2,3-triazole and carboxylate moieties were evaluated in vitro and by computational methods for their anti-diabetic potential to insig...
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Multi-spectroscopic and in silico investigation of gambogic acid–calf thymus DNA interactions J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-03 Boddapati Kalyani Bhardwaj, Arsha James, Jiya Tomy, Shalini K.B, Padmanaban S. Suresh
Gambogic acid (GA), a xanthanoid compound, is derived from Garcinia Hanbury gamboge resin. Studying GA's DNA binding and targeting processes is crucial to understanding its tumor-targeting potentia...
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Computational and in vitro screening validates the repositioning potential of Coxibs as anti-fibrotic agents J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-03 Shraddha Karande, Biswajit Das, Sushree Subhadra Acharya, Anoop Kumar, Harun Patel, Ajay Sharma, Madhu Gupta, Iqrar Ahmad, Vishwambhar Bhandare, Kalicharan Sharma, Chanakya Nath Kundu, Chandragouda Patil
Idiopathic pulmonary fibrosis (IPF) is a life-threatening disease with a survival rate of <5 years. The TGF-β plays a significant role in the progression and severity of IPF. The TGF-β receptor typ...
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Nano-gel formulation of polyphenolic fraction of tobacco stem for wound healing and its inhibitory efficacies against the receptors of chronic wound development J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-03-03 Yash Sharma, Rohit Bhardwaj, Amritpal Kaur, Gagandeep Singh, Sharvari Kulkarni, Amit Bhatia, Kumud Bala
Current investigation deals with the gel formulation of purified polyphenol loaded nanoparticles for enhanced wound healing. Polyphenols purified using column chromatography an were characterized u...
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Cracking a cancer code DNA methylation in epigenetic modification: an in-silico approach on efficacy assessment of Sri Lanka-oriented nutraceuticals J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-02-29 Dushanan R., Weerasinghe S., Dissanayake D. P., Senthilnithy R.
DNA methyltransferase (DNMTs) are essential epigenetic modifiers that play a critical role in gene regulation. These enzymes add a methyl group to cytosine’s 5'-carbon, specifically within CpG dinu...
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Discovery of novel bromodomain-containing protein 4 (BRD4-BD1) inhibitors combined with 3d-QSAR, molecular docking and molecular dynamics in silico J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-02-29 Rong Liu, Xiaodie Chen, Jiali Li, Xingyun Liu, Mao Shu
Bromine-containing domain protein 4 (BRD4) plays a crucial role in regulating transcription and genome stability. Selective inhibitors of BRD4-BD1 can specifically target specific bromine domains t...
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Toxoplasma gondii aspartic protease 5: structural basis of substrate binding and inhibition mechanism J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-02-29 Satadru Chakraborty, Anuradha Deshmukh, Pooja Kesari, Prasenjit Bhaumik
Toxoplasma gondii, a worldwide prevalent parasite is responsible for causing toxoplasmosis in almost all warm-blooded animals, including humans. Golgi-resident T. gondii aspartic protease 5 (TgASP5...
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C-30 analogues of betulinic acid as potent cytotoxic agents: design, synthesis, biological evaluation and in-silico studies J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-02-29 Santosh K. Rath, Rakesh K. Nagar, Sanjib Das, Govind Yadav, Debaraj Mukherjee, Buddh Singh, Samar Singh, Payare L. Sangwan
In an endeavour to improve the anti-cancer activity of betulinic acid (BA), a series of C-30 derivatives were envisaged and synthesized with a novel synthetic approach. All the derivatives were eva...
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Understanding the basis of thermostability for enzyme “Nanoluc” towards designing industry-competent engineered variants J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-02-28 Adwaita S. R. Nair, Arup Samanta, Saugata Hazra
As a leading contender in the study of luminescence, nanoluciferase has recently attracted attention and proven effective in a wide variety of research areas. Although numerous attempts have been m...
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Understanding a point mutation signature D54K in the caspase activation recruitment domain of NOD1 capitulating concerted immunity via atomistic simulation J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-02-28 P. Raghuraman, Sriroopreddy Ramireddy, Gurusamy Raman, SeonJoo Park, C. Sudandiradoss
Point mutation D54K in the human N-terminal caspase recruitment domain (CARD) of nucleotide-binding oligomerization domain −1 (NOD1) abrogates an imperative downstream interaction with receptor-int...
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Natural compounds inhibit Monkeypox virus methyltransferase VP39 in silico studies J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-02-28 Quynh Mai Thai, Huong T. T. Phung, Ngoc Quynh Anh Pham, Jim-Tong Horng, Phuong-Thao Tran, Nguyen Thanh Tung, Son Tung Ngo
VP39, an essential 2′-O-RNA methyltransferase enzyme discovered in Monkeypox virus (MPXV), plays a vital role in viral RNA replication and transcription. Inhibition of the enzyme may prevent viral ...
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Computational insights into KRAS G12C inhibition: exploring possible repurposing of Azacitidine and Ribavirin J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-02-28 Vishakha Sharma, Ankush Kumar, Ravi Rawat, Monica Gulati, Tapan Behl, Asaad Khalid, Asim Najmi, Khalid Zoghebi, Maryam A Halawi, Syam Mohan
Kirsten rat sarcoma (KRAS) stands out as the most prevalent mutated oncogene, playing a crucial role in the initiation and progression of various cancer types, including colorectal, lung and pancre...
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A hierarchical approach towards identification of novel inhibitors against L, D-transpeptidase YcbB as an anti-bacterial therapeutic target J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-02-27 Abdullah S. Alawam, Lina M. Alneghery, Maher S. Alwethaynani, Mubarak A. Alamri
The bacterial cell wall, being a vital component for cell viability, is regarded as a promising drug target. The L, D-Transpeptidase YcbB enzyme has been implicated for a significant role in cell w...
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A simulation-based approach to target Zika virus RNA-dependent RNA polymerase with marine compounds for antiviral development J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-02-28 Pradeep Sharma, Mahmoud Moustafa, Mohammed Al-Shehri, Faisal Alotaibi, Rima Bhardwaj, Indrakant K. Singh
Despite significant efforts, currently, there is no particular drug available to treat Zika virus (ZIKV) infection, highlighting the urgent need for effective therapeutic interventions. To identify...
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Identification of the odorant binding proteins of Western Flower Thrips (Frankliniella occidentalis), characterization and binding analysis of FoccOBP3 with molecular modelling, molecular dynamics simulations and a confirmatory field trial J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-02-28 Zeeshan Zafar, Martyn J. Wood, Sidra Fatima, Muhammad Faraz Bhatti, Farooq A. Shah, Zack Saud, E. Joel Loveridge, Ismail Karaca, Tariq M. Butt
Olfactory systems are indispensable for insects as they, including Western Flower Thrips (Frankliniella occidentalis), use olfactory cues for ovipositing and feeding. F. occidentalis use odorant bi...
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Efficiency of membrane fusion inhibitors on different hemagglutinin subtypes: insight from a molecular dynamics simulation perspective J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-02-28 Nadtanet Nunthaboot, Thitiya Boonma, Chananya Rajchakom, Bodee Nutho, Thanyada Rungrotmongkol
The challenge in vaccine development, along with drug resistance issues, has encouraged the search for new anti-influenza drugs targeting different viral proteins. Hemagglutinin (HA) glycoprotein, ...
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Anti-quorum sensing effects of SidA protein on Escherichia coli receptors: in silico analysis J. Biomol. Struct. Dyn. (IF 4.4) Pub Date : 2024-02-27 Mohsen Yazdani, Maria Beihaghi, Nazanin Ataee, Mahsa Zabetian, Samad Khaksar, Hanieh Nasrizadeh, Masoud Chaboksavar
Quorum sensing enables cell-cell communication in bacteria and regulates biofilm formation. Biofilm production promotes pathogenicity of Escherichia coli and causes infections. However, antibiotic ...