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The Juxtaposition of Allosteric and Catalytic Inhibition in PLK1: Tradeoff for Chemotherapy and Thermodynamic Profiles of KBJK557 and BI 6727 J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2024-01-25 Ernest Oduro-Kwateng, Ali H. Rabbad, Mahmoud E. Soliman
Polo-like kinase 1 (PLK1) is a serine/threonine kinase cell cycle modulator and a highly significant biomarker in chemotherapy. Cancer treatment strategies now prioritize PLK1-inhibitor-based drugs that target either the catalytic (kinase) or regulatory (polo-box) domains. Comparative studies on PLK1 are needed to highlight the tradeoff between catalytic- and allosteric-based inhibition. We report
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Molecular Dynamics Study on the Binding Characteristics and Transport Mechanism of Polysaccharides with Different Molecular Weights in Camellia Oleifera Abel. J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2024-01-19 Jihang Zhai, Fangfang Fan, Chaojie Wang, Zhiyang Zhang, Sheng Zhang, Yuan Zhao
α-Glucosidases catalyze the hydrolysis of the α-glucosidic bond located at the non-reducing ends of substrates, resulting in the release of glucose. α-glucosidase is an important drug target for controlling type 2 diabetes. Previous studies have shown that polysaccharide isolated and purified from Camellia oleifera Abel exhibits hypoglycemic properties. In this study, the mode in which the polysaccharide
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Computational Approach to Identify the Key Genes for Invasive Lobular Carcinoma (ILC) Diagnosis and Therapies J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2024-01-19 S. Anitha, S. Nandhini, D. Premnath, M. Indiraleka
Invasive Lobular Carcinoma (ILC) is a common form of breast cancer that begins in milk-producing glands lobules and spreads to other parts of the breast. According to the American Cancer Society, about 10–15% of breast cancer cases are ILC. ILC risk rises with age. The number of deaths caused by this cancer each year can be decreased through early diagnosis and if accurate therapy is given. However
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Exploring the Optical and Photovoltaic Changeover for Carbazole-Bridge Push-Pull Switches Against Their Local Excitations and Charge Transfers J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2024-01-19 Abrar U. Hassan, Sajjad H. Sumrra, Ayesha Mohyuddin, Muhammad Imran, Asad Ali
This research investigates characterization of low lying excitations of newly designed organic dyes for their local excited and charge transfer-related molecular switching attributes such as donor-acceptor relations against the carbazole bridge. The eight new dyes, having 4 symmetrical (Syn-A-D) and 4 antisymmetric (Anti-A-D) arrangements showed how the push-pull effect can operate to create the charge
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Computational Studies of Multi-Target Directed Ligands Against Acetylcholinesterase, Butyrylcholinesterase and Amyloid Beta as Potential Anti-Alzheimer’s Agents J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2024-01-03 Neha Maurya, Mareechika Gaddam, Abha Sharma
The designed flavone-hydroxypyridinone derivatives were screened in silico with the multiple targets of Alzheimer’s disease (AD) for their binding affinity. In this study, 29 novel derivatives of flavone-hydroxypyridinone were docked with acetylcholinesterase, butyrylcholinesterase and amyloid beta to determine their binding interactions on these targets of AD. The designed ligands were passed through
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Spatially Resolved Transcriptomics Reveals Local Invasion-Related Genes in Liver Hepatocellular Carcinoma: Exploring the Therapeutic Potential of a Chimeric Protein Targeting Glypican-3 J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2023-12-29 Muhammad Naveed, Hamza Jamil, Tariq Aziz, Syeda Izma Makhdoom, Abdulhakeem S. Alamri, Majid Alhomrani, Roaa Mohammed Tahir Kassim, Nehad. A Shaer, Aminah A. Barqawi, Nouf S. Al-Abbas
Despite advancements in cancer therapy, hepatocellular carcinoma (HCC) remains a major health concern due to late-stage diagnosis and poor prognosis. In this study, the expression of Glypican-3 (GPC3), a cell surface protein encoded by the GPC3 gene was analyzed at both Messenger RNA and protein levels. The goal was to advance understandings into the role of GPC3 in HCC progression and design a fusion
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Antifibromyalgic Activity of Phytomolecule Niranthin: In-Vivo Analysis, Molecular Docking, Dynamics and DFT J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2023-12-28 Atul R. Chopade, Vikram H. Potdar, Suraj N. Mali, Susmita Yadav, Anima Pandey, Chin-Hung Lai, Essa M. Saied, Oberdan Oliveira Ferreira, Mozaniel Santana de Oliveira, Shailesh S. Gurav, Eloisa Helena de Aguiar Andrade
Fibromyalgia (FM) is characterized by chronic pain and heightened sensitivity to painful stimuli. This study investigated the potential of Niranthin (NR), a natural compound derived from Phyllanthus species, in a rat model of FM. We employed a multifaceted approach to comprehensively assess the potential benefits of NR as a treatment for FM, including in-vivo analysis, molecular docking studies, and
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Assessment of Melia azedarach Plant Extracts Activity Against Hypothetical Protein of Mycobacterium tuberculosis via GC-MS Analysis and In Silico Approaches J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2023-12-14 Muhammad Naveed, Imran Ali, Tariq Aziz, Nouman Ali, Ali Hassan, Shafiq Ur Rahman, Riffat Aziz, Metab Alharbi
Medicinal plants have played an important role in treating different diseases. Melia azedarach is a plant with significant medical and biological applications. This research aimed to explore the possible bioactivity of various biological compounds. The gas chromatography-mass spectrometry (GC-MS) analysis of Melia azedarach identified 25 compounds, among which 1-ethyl-3-methyl-2-nitrosobenzene and
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A DFT Study on the Impact of Saturated and Conjugated Side Chains on the Optoelectronic Performance of Y-series Nonfullerene Acceptors J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2023-08-22 Fareeda Kalsoom, Umar Farooq, M. Salman, Riaz Hussain
Organic photovoltaic (OPV) consisting of nonfullerene acceptors have been found to be excellent candidates for harnessing solar energy. Extensive studies are being carried out to modify structures in a number of ways to enhance their efficiency. These include modifications in the acceptor part, use of efficient backbones and insertion of pi spacers. One strategy is the attachment of donor side chains
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A Multi-target Study of Natural Compounds in Preventing Neurodegenerative Disease Progression: A Computational Modeling Study J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2023-08-22 Yuri Alves de Oliveira SÓ, MÔnica de Abreu Silva, Alessandra Sofia Kiametis, Camila D’Avila Braga Sette, Marcelo Lopes Pereira Junior, Luiz Antônio Ribeiro Júnior, Ricardo Gargano
This work reveals how two natural multi-target compounds (Carnosine and Homocarnosine) can prevent the oligomerization of beta-amyloid peptides (Aβ). Properly combining molecular dynamics, docking and electronic structure calculations it was possible to investigate how Carnosine/Homocarnosine strongly interact with the amino acids of the Aβ(1-42) peptide responsible for the complexation with metallic
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In Silico Analysis of Phytocompounds from Aegle marmelos Against Potential Targets of Irritable Bowel Syndrome J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2023-08-17 Gopikrishna Gopakumar, Bhavani Ramesh, Drose Ignatious Shane Michaelson, Selvaraj Kunjiappan, Shanmugampillai Jeyarajaguru Kabilan, Parasuraman Pavadai
Irritable Bowel Syndrome (IBS) is a gastrointestinal disorder that affects 7-21% of the world’s population. People suffering from this illness can have a significant change in their quality of life and their productivity at work. Medicinal plants and their derived products have long been explored and used for their medicinal qualities throughout the world to cure numerous ailments, including gastrointestinal
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Electronic and NLO Performances of Benzohydrazide Derivatives: DFT Investigation and (RDG, AIM) Analysis J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2023-08-07 Nadia Benhalima, Bendouma Doumi, Oumria Kourat, Fatima Yahia Cherif, Nour El Houda Daho, Abdelkader Chouaih, Adlane Sayede
DFT calculations of ground-state hydrazine and benzohydrazide derivatives were performed by using hybrid functional B3LYP and CAMB3LYP with 6–31G (d, p) as basis set. The electric dipole moment (μ), polarizability (α) and molecular first hyperpolarizability (β) were characterized in these compounds. The HOMO–LUMO energy gaps and the global chemical reactivity descriptors were computed by B3LYP and
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Computational Insight into Electronic, Optical and Photophysical Properties of Small Compounds for Solar Cell Applications J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2023-07-26 Aijaz Rasool Chaudhry, Yahia A. H. Obaidat, Shabbir Muhammad, Saifedin Y. DaifAllah, Bakhtiar Ul Haq
Thiophene-based small molecules COMP.1 and COMP.2 are explored for optical, electronic and photophysical properties by using theoretical approach. The density functional theory (DFT) at B3LYP/6-31G** level of theory is used to optimize both molecules COMP.1 and COMP.2 at ground state, while for excited state, the time-dependent DFT (TD-DFT) is utilized at the same level of theory. The optoelectronic
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Modeling of Conjugated Core-Based Non-Fullerene Acceptor Materials for Organic Photovoltaic Applications J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2023-07-26 Muhammad Adnan, Muhammad Faisal, Riaz Hussain, Muhammad Usman Khan, Junaid Yaqoob, Fakhar Hussain, Sabir Ali Siddique, Umar Farooq, Churl-Hee Cho, Jongchul Lim
Non-Fullerene acceptors (NFAs) are attracting much attention from scientists worldwide for their potential use in organic solar cells (OSC). Herein, we developed C-shaped NFAs acceptors (FA1–FA10) by performing end-capped alteration on GL1. The structural-property relation and optoelectronic characteristics were examined theoretically. Furthermore, the impact of structural changes on the optoelectronic
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Computational Analysis and Rational Design of N-Substituting Perturbation on the Affinity and Specificity of Pediatric Fyn SH3–Peptoid Interaction J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2023-07-26 Qin Liu, Jie Wang, Lin Shi, Xiang Shao
Human nonreceptor tyrosine kinase (TK) Fyn is implicated in various cellular processes and has been exploited as a sophisticated druggable target of pediatric T-cell lymphoma by blocking its kinase domain with small-molecule inhibitors or disrupting its regulatory SH2 and SH3 domains with peptidic inhibitors. In this study, the proline-heavy 9P1Y-peptide was found as a good binder of Fyn SH3 domain
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Synthesis, In-Silico, In Vitro and DFT Assessments of Substituted Imidazopyridine Derivatives as Potential Antimalarials Targeting Hemoglobin Degradation Pathway J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2023-07-26 Oberdan Oliveira Ferreira, Suraj N. Mali, Bhagwat Jadhav, Samir Chtita, Aleksey Kuznetsov, Richie R. Bhandare, Afzal B. Shaik, Farhan Siddique, Akshay R. Yadav, Chin-Hung Lai, Jorddy Neves Cruz, Eloisa Helena de Aguiar Andrade, Snehal Arvindekar, Rahul D. Jawarkar, Mozaniel Santana de Oliveira
Malaria is a serious illness transmitted through the bite of an infected mosquito, which is caused by a type of parasite called plasmodium and can be fatal if left untreated. Thus, newer antimalarials with unique mode of actions are encouraged. Fused pyridines have been vastly reported for numerous pharmacological activities including but not limited to analgesics, antitubercular, antifungal, antibacterial
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A DFT Study of Bridge-Driven Engineering of Non-Fullerene-Based Acceptors for Efficacious Organic Solar Cell Applications J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2023-07-25 Ali Raza Ayub, Umer Yaqoob, Sidra Rafiq, Salba Arshad, Muhammad Umar Dad, Hui Li
The structural, optical, electronic and photovoltaic properties of non-fullerene molecular entity were analyzed by using density functional theory method MPW1PW91/6-31G (d, p). The simulated results of all the modeled molecules proved them as more efficient molecules for practical use in organic solar cell. Their good solution process-ability and interface (new modeled molecules: PBDBT) success made
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Molecular Dynamics Studies of Mixtures of a Deep Eutectic Solvent and Cosolvents J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2023-07-25 Deepak Kumar Panda, B. L. Bhargava
All-atom molecular dynamics simulations have been performed on mixtures of tetrabutylammonium chloride-based deep eutectic solvent and two cosolvents — methanol and acetonitrile. Water, a highly polar protic solvent, strongly interacts with the DES components. Herein, we have chosen methanol, a protic solvent but less polar than water, and acetonitrile, an aprotic solvent, to investigate the structural
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Closed-Loop Deep Brain Stimulation Using a Type of Fixed-Time Sliding Mode Controller for Avoiding Epileptiform Discharge in a Human Cortical Model J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2023-07-25 Sajad Mohammad-Ali-Nezhad, Samira Rezvani-Ardakani, Reza Ghasemi
The cortical excitability rate correlates with epileptic seizures, which should be modulated in a finite time to prevent brain damage. Deep brain stimulation (DBS) is a successful treatment for patients with refractory epilepsy. This study proposes a closed-loop DBS control method that uses a Fixed-Time Integral Super-Twisting Sliding Mode Controller (FTISTSMC) to stop simulated epileptiform discharges
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Exploring Key Proteins, Pathways and Oxygen Usage Bias of Proteins and Metabolites in Melanoma J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2023-07-22 Man Zhang, Chengxu Zhu, Zeyu Luo, Junhao Liu, Muhammad Tahir Khan, Yawen Sun, Dong-Qing Wei, Yu-Juan Zhang
Hypoxia plays a critical role in melanoma development, but the characteristics of elemental oxygen in proteins and adaptation to hypoxia microenvironments are still unidentified. This study aims to explore oxygen contents (OCs) and differentially expressed proteins (DEP). Protein expression data were retrieved from Human Protein Atlas. The DEP in melanoma samples were compared with normal skin cells
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In Silico Studies, Design and Synthesis of Novel Fused Pyrimidine Derivatives as a DNA Gyrase Inhibitor and Antibacterial Activity Against Quinolone Resistant Escherichia Coli J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2023-07-21 Richie R. Bhandare, N. Helina, Arun kumar Subramani, Ramalakshmi Natarajan, Suraj N. Mali, Afzal B. Shaik
In recent years, antimicrobial agents have been crucial in improving public health worldwide. However, due to improper usage, bacteria have developed resistance to these agents. This has led researchers to explore the use of heterocyclic compounds as alternative antimicrobial agents to combat resistance. Considering the success of heterocyclic derivatives in developing effective antimicrobial drugs
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Role of Aromatic Heterocyclic Core-Based Materials as Donorsfor Organic and as Hole-Transporting Materials for Perovskites Solar cells J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2023-07-17 Muhammad Adnan, Qandeel Fatima, Zobia Irshad, Riaz Hussain, Junaid Yaqoob, Muhammad Usman Khan, Nooruddin Ansari, Sabir Ali Siddique, Jongchul Lim
Hole-transporting materials (HTMs) have revolutionized the field of photovoltaics for solar cell devices. Herein, novel butterfly-shaped hole transport material (HTM) 2,7-DMPZ (R) containing twisted core unit is used to develop novel molecules (Q1–Q6) by fitting suitable donor groups at peripheral regions of 2,7-DMPZ. To investigate the power conversion efficiency (PCE) of Q1–Q6, different analyses
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Effects of Angiotensin 1-7 Binding on the Dynamics of Human MAS Proto-Oncogene, GPCR: A Molecular Dynamics Study J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2023-07-06 Ekrem Yasar, M. Murat Yasar, Segun Dogru, Nazmi Yaras, Erol Eroglu
The understanding of the connections between Angiotensin peptides with the receptors in the Renin-angiotensin system (RAS) is not clear yet. The ACE2/Ang (1-7)/MAS axis, commonly referred to as the protective arm of the RAS, plays a crucial role in maintaining homeostasis within the cardiovascular system. Angiotensin 1-7 (Ang 1-7) is a heptapeptide an integral part of the protective arm of RAS and
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Anti-Tuberculous Drug Copper Pyrazinamide: Synthesis, Characterization, Theoretical DFT, Bioactivity and Toxicity Studies in the Liver J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2023-06-22 Margaret D. Olawale, Fausat K. Ola-Mudathir, Eric O. Akintemi, Joshua A. Obaleye
Mycobacterium tuberculosis causes tuberculosis, an infectious disease. Pyrazinamide is a tuberculosis treatment. Metal–ligand–drug complexation can be used to improve the therapeutic efficacy of drugs. Copper pyrazinamide (CuPZA), a newly synthesized drug, is being considered for tuberculosis treatment. CuPZA was synthesized by soft synthetically reacting Cu (II) metal with pyrazinamide. The metal-drug
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In-silico Design of Curcumin Analogs as Potential Inhibitors of Dengue Virus NS2B/NS3 Protease J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2023-06-10 Miah Roney, AKM Moyeenul Huq, Mohd Fadhlizil Fasihi Mohd Aluwi, Saiful Nizam Tajuddin
Curcumin can interact with a variety of molecules implicated in a wide range of disorders. It can also hinder dengue virus’s (DENV’s) ability to infect cells. This work used computational analysis to identify and forecast the most potent curcumin analogs against the DENV NS2B/NS3 protease. In this study, curcumin-like compounds were screened using a rational in-silico study, with the least similarity
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Hydrocarbon Stapling-Improved Coupled Folding-Upon-Binding of Peptide-Mediated Interaction between the Nucleocapsid and Phosphoprotein of Human Orthopneumovirus J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2023-06-10 Jianqiang Shen, Meiyuan Chen, Jianqin Chen, Jiangang Wu, Yan Shen, Yumei Chen, Zhaohui Wang
Human orthopneumovirus (OPV) is a common respiratory virus that mostly causes respiratory illness in children. Development of therapeutic strategies to treat OPV infection has attracted considerable interest in the medicinal and biological communities. Over the past decades, significant effects have been addressed on disrupting membrane fusion events by targeting viral fusogenic glycoprotein (F-protein)
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3D-QSAR and Molecular Docking Studies of Novel GPR52 Agonists J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2023-06-10 Qingshan Gu, Jingxuan Hou, Hui Gao, Meiqi Shi, Ying Zhuang, Qingkun Wu, Lu Zheng
To study the three-dimensional quantitative structure–activity relationship (3D-QSAR) of a series of GPR52 agonists, comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) were used to establish 3D-QSAR models. The cross-validation coefficient (q2), non-cross validation coefficient (r2) and standard error of estimate (SEE) of the constructed CoMFA
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Assessment of the Capability and Potential of Pristine, Sc-, Ti-, and Ni-Doped C24 Nanocages to Delivery and Sensor Property of Prothionamide Drug: Insight of DFT, TD-DFT Computational Methods J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2023-06-08 M. Rezaei-Sameti, H. Torabi
The capability and potential of C24, ScC23, TiC23, and NiC23 nanocages as novel candidates for delivery and sensor property of the Prothionamide (PA) drug in a biological system are investigated with density functional theory. The adsorption energy and thermodynamic parameters of [email protected]24, [email protected]23, [email protected]23, and [email protected]23 complexes in the absences and presence
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Persistent Topological Laplacian Analysis of SARS-CoV-2 Variants J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2023-06-08 Xiaoqi Wei, Jiahui Chen, Guo-Wei Wei
Topological data analysis (TDA) is an emerging field in mathematics and data science. Its central technique, persistent homology, has had tremendous success in many science and engineering disciplines. However, persistent homology has limitations, including its inability to handle heterogeneous information, such as multiple types of geometric objects; being qualitative rather than quantitative, e.g
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LSDDB: Lysosomal Storage Disorder Database for Lysosomal Proteins and Their Single Amino-Acid Substitutions J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2023-05-26 D. Meshach Paul, G. Chandrasekhar, E. Srinivasan, P. Chandra Sekar, B. Udhaya Lavinya, R. Rajasekaran
Lysosomal storage diseases (LSDs) consist of about 60 different monogenic disorders. Most of them occur due to protein misfolding. Only a few of those have been treated with molecular chaperones; the remaining either have limited treatment options or only management therapies. About 1860 single amino-acid substitutions (SAS) have been identified under LSDs. Merely, a handful of mutations have been
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Designing Potential Inhibitors of SARS-CoV-2 Mpro Using Deep Learning and Steered Molecular Dynamic Simulations J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2023-05-06 Nguyen Minh Tam, Linh Hoang Tran, Quan V. Vo, Minh Quan Pham, Huong Thi Thu Phung
The COVID-19 pandemic raised an unprecedented race in biotechnology in search for effective therapies and a preventive vaccine. Scientists worldwide have been attempting to stop the viral infection by interfering with the biological function of the SARS-CoV-2 main protease (Mpro), a critical protein required for viral transcription and replication during infection. In this study, we employed an effective
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MembIT – A Tool to Calculate Solute Membrane Insertions and Deformations in Molecular Dynamics Simulations J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2023-04-29 Pedro M. S. Suzano, Inês D. S. Pires, Tomás F. D. Silva, Nuno F. B. Oliveira, Pedro B. P. S. Reis, Miguel Machuqueiro
In molecular dynamics simulations of membrane systems, it is very important to evaluate the interactions between membrane bilayers and other molecules like small compounds, peptides, or proteins. When these interactions lead to local deformations in the membrane, it is essential to fully understand and accurately characterize them, since these deformations can impact the calculation of membrane properties
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Developing High-Resolution Metastasis Signatures for Improved Cancer Prognosis and Drug Sensitivity Prediction using Single-Cell RNA Sequencing Data: A Case Study in Lung Adenocarcinoma J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2023-04-28 Yeman Zhou, Hanlin Li, De’en Yu, Cheng Zhang, Heng Yang, Chunping Wang, Youhua Zhang, Wensheng Deng, Bo Li, Shihua Zhang
Metastasis remains the reason for chemoresistance and high cancer mortality. It is hence a valuable predictive factor in cancer prognosis and drug sensitivity. Single-cell RNA sequencing (scRNA-seq) can reveal cellular heterogeneity in metastasis microenvironment and capture high-resolution signatures for improved cancer prediction. As a case study, an integrated analysis framework was designed for
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PKAD-2: New Entries and Expansion of Functionalities of the Database of Experimentally Measured pKa’s of Proteins J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2023-04-25 Nicolas Ancona, Ananta Bastola, Emil Alexov
Almost all biological reactions are pH-dependent and understanding the origin of pH dependence requires knowledge of the pKa’s of ionizable groups. Here, we report a new edition of PKAD, the PKAD-2, which is a database of experimentally measured pKa’s of proteins, both wild-type and mutant proteins. The new addition includes 117 wild-type and 54 mutant pKa values, resulting in total 1742 experimentally
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Computational Analysis of Mixed Convection in a Blood-Based Hybrid Nanoliquid under Boussinesq Approximation in a Transient Regime J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2023-04-06 Ebenezer Olubunmi Ige, Bidemi Olumide Falodun, Daniel Oluwamuyiwa Adebiyi, Sami Ullah Khan
In recent times, nanoparticle-embedded flows are becoming household fluid in emerging medical interventions associated with thermal therapy. The place of thermal analysis is critical to underscore the potential of bio-nanofluidics and to perform a biothermal mechanical analysis of its performance during remediation strategies. This paper presents a thermal expedition of a hybrid nanofluid embedded
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Assessments of Variational Autoencoder in Protein Conformation Exploration J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2023-03-27 Sian Xiao, Zilin Song, Hao Tian, Peng Tao
Molecular dynamics (MD) simulations have been extensively used to study protein dynamics and subsequently functions. However, MD simulations are often insufficient to explore adequate conformational space for protein functions within reachable timescales. Accordingly, many enhanced sampling methods, including variational autoencoder (VAE) based methods, have been developed to address this issue. The
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Neighborhood Path Complex for the Quantitative Analysis of the Structure and Stability of Carboranes J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2023-03-20 Jian Liu, Dong Chen, Feng Pan, Jie Wu
Thanks to the tremendous progress in data, computing power and algorithms, AI-based material mining and design have gained much attention. However, building high-performance AI models requires efficient material structure representation. In this work, we propose a structural characterization method based on the neighborhood path complex for the first time. Specifically, we use persistent neighborhood
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In Silico Study of Thiourea Derivatives as Potential Epidermal Growth Factor Receptor Inhibitors J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2023-03-02 Norashikin Roslan, Khairul Bariyyah Abd. Halim, Noraslinda Muhamad Bunnori, Mohd Fadhlizil Fasihi Mohd Aluwi, Karimah Kassim, Nurziana Ngah
Over the years, the escalation of cancer cases has been linked to the resistance, less selectivity, and toxicity of available anticancer drugs to normal cells. Therefore, continuous efforts are necessary to find new anticancer drugs with high selectivity of epidermal growth factor receptor tyrosine kinase (EGFR-TK) as a therapeutic target. The EGFR-TK protein has a crucial role in cell proliferation
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In Silico Identification of Triclosan Derivatives as Potential Inhibitors of Mutant Mycobacterium tuberculosis InhA J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2023-02-25 Nasrin Panahi, Nima Razzaghi-Asl
Enoyl acyl carrier protein reductase (InhA) is a crucial enzyme for the biosynthesis of mycolic acids which are major compartments of the Mycobacterium tuberculosis (Mtb) cell wall. Direct inhibition of InhA without activation by drug-NADH adduct has clinical utility to overcome drug resistance. We aimed at the in silico identification of triclosan derivatives with the potential inhibitory effect of
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Development of Highly Viscous Multiphase Fluid Flows: Towards an Approximate Analysis J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2023-02-20 Mubbashar Nazeer, Farooq Hussain, Mustafa Türkyılmazoğlu, M. A. Javed, Qasiar Shahzad
Two separate types of multiphase flow models have been developed theoretically in this paper. Fourth-grade fluid model of non-Newtonian in nature is considered the main carrier. Silver and gold metallic particles of spherical shape suspend to form highly viscous multiphase flows which drift through an inclined channel. Effects of magnetic fields acting across the channel are applied as the body force
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Negishi or Suzuki–Miyaura Pd-Catalyzed Cross-Coupling Reaction: Which Reaction Mechanism is Ahead for the Formation of Well-Known Anticancer Drug Combretastatin A-4 Analogue? J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2023-02-20 Zeinab Ahmadvand, Mehdi Bayat
In recent years, scientists have become increasingly interested in finding high-efficacy, low-toxicity anti-tumor compounds. Combretastatin A-4 (CA-4) is supposed to be one of the materials that has excellent anti-tumor properties. This study intends to develop a more acceptable pathway and cross-coupling mechanism to resolve the contest between Negishi and Suzuki–Miyaura cross-coupling to form a combretastatin
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Use of Apatinib as a Bait to Fish its Unexpected Kinase Targets from the Hepatocellular Carcinoma Druggable Kinome J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2023-02-20 Rui Liu, Lijun Liu
Apatinib is a tyrosine kinase inhibitor that cognately blocks the kinase activity of vascular endothelial growth factor receptor (VEGFR) signaling for the treatment of advanced gastric cancer (GC). However, the drug is also clinically found to reposition a significant suppressing potency on hepatocellular carcinoma (HCC). In this study, we reported the successful use of Apatinib as a bait to fish its
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Unsteady MHD Flow of Casson Fluid Past Vertical Surface Using Laplace Transform Solution J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2023-02-18 Farhan Ali, A. Zaib, M. Khalid, T. Padmavathi, B. Hemalatha
The study explores the velocity of Casson fluid that is time-independent over an exponentially infinite isotherm vertical permeable sheet. The impact of magnetohydrodynamic (MHD) with Casson flow over the permeability sheet is examined. In contrast, thermal radiation and heat sink parameters have been incorporated. This study’s primary goal is to determine the significance of thermal radiation on Casson
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SARS-CoV-2 Main Protease Inhibitors: Structure-Based Enhancement to Anti-Viral Pre-Clinical GC376 Encourages Further Development J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2023-02-08 Elliot D Perry, Simon Chapman, Yao-Zhong Xu
SARS-CoV-2 Main protease (Mpro) is pivotal in viral replication and transcription. Mpro mediates proteolysis of translated products of replicase genes ORF1a and ORF1ab. Surveying pre-clinical trial Mpro inhibitors suggests potential enhanced efficacy for some moieties. Concordant with promising in vitro and in silico data, the protease inhibitor GC376 was chosen as a lead. Modification of GC376 analogues
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Exploration of Newtonian Heating, Viscous Dissipation Effects on MHD Mixed Convection Flow of Williamson Fluid Against Radially Stretched Penetrable Wedge: A Numerical Study J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2023-02-03 Majid Hussain, Mehwish Ashraf, Qasim A. Ranjha, Mustafa Inc, Shah Jahan
An investigation on framing the features of Newtonian heating, suction/blowing, viscous dissipation on magneto hydrodynamic mixed convective Williamson fluid flow over a porous stretching wedge that is influenced by thermal radiation. The con-temporary model is employed to simulate the non-Newtonian behavior of fluid over porous wedge which stretches faster or slower than free stream velocity. Practical
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Computational Study on D-π-A-Based Metal-Free Donor-Tuned Molecules for Efficient Organic Dye-Sensitized Solar Cells J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2023-01-28 S. Aadheeswari, P. M. Anbarasan, A. Arunkumar, Mohd Shkir
In this paper, newly metal-free four donor-π-acceptor (D-π-A) molecules (C1D1–C1D4) were designed and used for dye-sensitized solar cells (DSSCs) application, based on literature C1-1. Tetrahydroquinoline, thiophene, and 2-cyanoacrylic acid act as the electron-D, spacer, and electron-A/anchoring groups for all dyes, respectively, while the donor part was tuned and the effect was examined. The density
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Structural Insights into the Interactions of Belumosudil with Rho-Associated Coiled-Coil Containing Protein Kinases 1 and 2 Based on Molecular Docking, Molecular Dynamics Simulations, and Free Energy Calculations J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2023-01-28 Mingsong Shi, Jiang Liu, Suhong Fu, Heying Pei, Bin Peng, Yi Wen, Haoche Wei, Xin Zhou, Lijuan Chen, Dingguo Xu
Rho-associated coiled-coil containing protein kinases (ROCKs) are members of the cyclic adenosine monophosphate-dependent protein kinase/protein kinase G/protein kinase C family that participates in a variety of important physiological functions, including smooth muscle contraction, cell proliferation, cell adhesion, migration, and inflammatory responses. In this study, we focused on ROCK1 and ROCK2
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Selectivity Mechanism of Hsp90 Isoform Inhibition Through Computational Investigation J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2022-12-28 Hanqing Xu, Hanxun Wang, Baichun Hu, Yinli Gao, Lanlan Shen, Jian Wang
The Hsp90 family has been extensively studied as a promising target against cancer and neurodegenerative diseases due to its crucial role in protein maturation and transport. However, the toxic and side effects such as cardiotoxicity and ocular toxicity caused by the pan-inhibition of Hsp90 cannot be ignored. The development of highly selective inhibitors toward Hsp90α over Grp94 has been proved to
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Computational Screening of D-π-A Structured with Acceptor-Tuned Metal-Free Organic Dye Molecules for DSSCs J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2022-12-28 A. Arunkumar, P. M. Anbarasan, Mohd Shkir, V. Balasubramani
Four metal-free carbazole-based acceptor-tuned organic molecules (denoted as CBa1–CBa4) based on electron-donor, π-spacer and electron-acceptor (D-π-A) for dye-sensitized solar cells (DSSCs) have been newly designed. The electronic structures, optical absorption ultraviolet-visible (UV–Vis) properties and photovoltaic (PV) parameters of CBa1–CBa4 dyes were computationally studied by the density functional
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Thermodynamics and Heat Transfer Analysis of Magnetized Casson Hybrid Nanofluid Flow via a Riga Plate with Thermal Radiation J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2022-12-27 Himanshu Upreti, Alok Kumar Pandey, Navneet Joshi, O. D. Makinde
The importance of non-Newtonian fluid (Casson fluid) in industry is increasingly appreciated. However, little is known about the flow rheology of Casson fluid flowing over a Riga plate. Thus, the purpose of this investigation is to examine the nature of entropy generation (EG) and heat transfer (HT) on Casson hybrid nanofluid flow past a Riga plate by considering the influences of magnetic field and
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Theoretical Studies on OH−+NH2Cl Reaction: Nucleophilic Substitution at Neutral Nitrogen J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2022-12-23 Rui Li, Xu Liu, Boxue Pang, Hui Li, Yang Wu
The SN2 and proton transfer (PT) pathways for OH−+NH2Cl reaction are represented by employing various electronic structure computations. Both back-side SN2 and PT channels are exothermic and stationary points of PESs are below the reactant asymptote. Overall, the PES is similar to the C-centered SN2 reactions. Conversely, ion-dipole complex was not found for OH−+NH2Cl system. The N–HOH/NH–Cl hydrogen
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Determining Zn(II) Binding Affinities of the YiiP–Zinc Transporter and Uno Ferro Single Chain (UFsc) Protein with a Novel Modification of the PKA17 Software J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2022-12-23 George A. Kaminski, Greggory W. Raymond
In this paper, we report results of using molecular modeling to assign specific Zn(II) binding affinities to the known binding sites of the YiiP–zinc transporter. YiiP is a cation-diffusion facilitator. It facilitates the transmembrane exchange of Zn(II) ions and protons. The crystal structure of this protein is known. There are several zinc binding sites, and some of the Zn(II) binding affinities
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Bioinformatics and Molecular Dynamics Studies on the Human DISC1 in Complex with the Ndel1 J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2022-12-21 Mohammad Yaghoubzad-Maleki, Saba Habibi, Emran Heshmati, Khosrow Khalifeh
In this study we analyzed the sequence and structure of the human DISC1-Ndel1 complex using bioinformatics tools and molecular dynamics simulation studies. Multiple sequence alignment between the homologue protein sequences in primates shows that corresponding positions of residues in Ndel1 are highly conserved, while the DISC1 has variable conservation lines demonstrating its tolerability against
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Designing Superalkali Metals-Doped Sumanene-Based Highly Efficient Nonlinear Optical Materials for Cutting-Edge Optoelectronic Applications J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2022-12-17 Azka Asif, Ghulam Mustafa, Junaid Yaqoob, Muhammad Usman Khan, Mohammed A. Assiri, Muhammad Imran
Nonlinear optical (NLO) materials have attracted bounteous scientific attention in the modern era because of their optoelectronic and biological applications. In this respect, an attempt is made to present thermodynamically stable superalkali metals (Li3N, Li3O, Li3S and Li3F)-doped sumanene (C21H12)-based complexes with fine NLO response properties. Nine isomers (I–III of Li3[email protected], I–II
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Alkali and Transition Metal-Doped 15-Crown-5 with Enhanced Nonlinear Optical Response: A DFT Study J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2022-12-15 Naima Rafique, Hillia Fatima, Muhammad Ans, Khurshid Ayub, Javed Iqbal
In this study, geometries, electronic structure and first hyperpolarizability of metals doped 15-crown-5 (C5M) were explored through the density functional theory (DFT) method. Alkali metals (Li, Na, K) and silver (Ag) were placed inside and outside of the crown ether, respectively, to deliver three compounds designated as Li[C5M]Ag, Na[C5M]Ag and K[C5M]Ag. All designed complexes were optimized at
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Integrated in Silico–in Vitro Rational Design of Osteogenic Peptides derived from the Armpit Epitope of Human Bone Morphogenetic Proteins J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2022-12-08 Fangguo Li, Xi Zhang, Yandong Lu, Lei Chen, Jie Sun
Bone morphogenetic proteins (BMPs) are multi-functional growth factors that initiate, promote and maintain cartilage and bone morphogenesis, differentiation and regeneration in both the developing embryo and adult. The proteins have a conformational wrist epitope and a linear knuckle epitope responsible for, respectively, type-I and type-II receptor binding, as well as a hybrid armpit epitope targeted
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Unveiling Attributes of Human 15-Lipoxygenase-1 as a Potential Candidate for Prostate Cancer Drug Development Using in Silico Approaches J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2022-11-30 Shirin Fathi, Amirhossein Sakhteman, Aida Solhjoo
Prostate carcinoma is one of the most commonly diagnosed visceral malignancies and the fifth leading cause of cancer-related mortality in males. Reportedly, a series of dietary lipids are identified as 1-cis-4-cis-pentadiene polyunsaturated fatty acids (PUFAs), which play a dominant role in prostate carcinogenesis. Four species of human lipoxygenases (LOXs), a family of nonheme iron-containing enzymes
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Stratified Bioconvective Jet Flow of Williamson Nanofluid in Porous Medium in the Presence of Arrhenius Activation Energy J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2022-11-25 V. Puneeth, S. Manjunatha, M. Shoaib Anwar, Mowffaq Oreijah, Kamel Geudri, Omar T. Bafakeeh, Ahmed M. Galal
Due to the higher coefficients of heat and mass transfer, the jet flow has become an effective source for the transfer of heat and mass in various industries. Due to these high coefficients, the heat and mass transfer rates will be high in the appliances equipped with the jet flow. Further, the existence of the magnetic field helps in controlling the velocity and the presence of the gyrotactic microorganisms
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Identification of Novel 5-Lipoxygenase-Activating Protein (FLAP) Inhibitors by an Integrated Method of Pharmacophore Virtual Screening, Docking, QSAR and ADMET Analyses J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2022-11-25 Kamal Rullah, Miah Roney, Zalikha Ibrahim, Nur Farisya Shamsudin, Deri Islami, Qamar Uddin Ahmed, Kok Wai Lam, Mohd Fadhlizil Fasihi Mohd Aluwi
This study explored a series of reported 5-lipoxygenase-activating protein (FLAP) inhibitors to understand their structural requirements and identify potential new inhibitor scaffolds through automated unbiased procedures. Docking studies have revealed that inhibitor binding affinity can be influenced by several key binding interactions with Phe114 and Lys116 from chain B and Val21, Phe25, His28 and
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The Binding Behavior of Peptide Ligands to Human Osteoclast-Stimulating Factor SH3 Domain Shifted by a Rationally Designed π-Stacking System J. Theor. Comput. Chem. (IF 2.4) Pub Date : 2022-11-18 Qi Huang, Xianquan Xu, Xiaoting Song, Dun Hong
Human osteoclast-stimulating factor (OSF) induces osteoclast formation and bone resorption in osteoporosis by recruiting multiple signaling complexes with downstream partners. Protein contains a peptide-recognition Src homology 3 (SH3) domain that can recognize and bind class II linear motif P−1xxP+2x[K∕R]+4 to its partner proteins. The motif is defined by two prolines at positions −1 and +2, which