Article
Chemistry, Medicinal
Giavana R. Prucha, Sean Henry, Klarissa Hollander, Zachary J. Carter, Krasimir A. Spasov, William L. Jorgensen, Karen S. Anderson
Summary: This study reports the synthesis of 34 compounds that covalently inhibit reverse transcriptase to overcome the issue of resistance to non-nucleoside reverse transcriptase inhibitors. Two of these inhibitors demonstrate biochemical, structural, enzyme kinetic, mass spectrometry, and antiviral activity against HIV-1.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Article
Virology
Maria E. Cilento, Xin Wen, Aaron B. Reeve, Obiaara B. Ukah, Alexa A. Snyder, Ciro M. Carrillo, Cole P. Smith, Kristin Edwards, Claudia C. Wahoski, Deborah R. Kitzler, Eiichi N. Kodama, Hiroaki Mitsuya, Michael A. Parniak, Philip R. Tedbury, Stefan G. Sarafianos
Summary: TDF and ISL are highly potent nucleoside reverse transcriptase inhibitors with different resistance profiles. This study found that ISL is sensitive to the K65R mutation, while TDF is sensitive to the M184V mutation. The sensitivity to these drugs also varies among different HIV subtypes, and the S68G polymorphism may enhance the fitness of drug-resistant mutants in certain genetic backgrounds.
Article
Cell & Tissue Engineering
Adrian Farid Elzarki, Seshagiri Rao Nandula, Hassan Awal, Gary L. Simon, Sabyasachi Sen
Summary: The study suggests that an INSTI-based regimen may have a better impact on cardiovascular disease (CVD) risk in HIV+ patients compared to an NNRTI-based HAART regimen. However, the increased levels of urine microalbumin and lower eGFR in the INSTI group are concerning.
STEM CELL RESEARCH & THERAPY
(2022)
Article
Chemistry, Medicinal
Xiangyi Jiang, Boshi Huang, Waleed A. Zalloum, Chin-Ho Chen, Xiangkai Ji, Zhen Gao, Jiaojiao Dai, Minghui Xie, Dongwei Kang, Erik De Clercq, Christophe Pannecouque, Xinyong Liu, Peng Zhan
Summary: Novel diarypyrimidine derivatives were designed based on previously reported HIV-1 NNRTIs BH-11c and XJ-10c to improve antiresistance and drug-like profiles. Compound 12g showed the highest inhibitory activity against wild-type and NNRTI-resistant HIV-1 strains, with EC50 values ranging from 0.024 to 0.0010 μM. Its improved antiresistance profile compared to ETR was explained by MD simulation study and it also showed improved water solubility and other drug-like properties. Compound 12g exhibited promising pharmacokinetics parameters and could be a potential lead compound for new antiretroviral drug development.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Mahta Mansouri, Shawn Rumrill, Shane Dawson, Adam Johnson, Jo-Anne Pinson, Menachem J. Gunzburg, Catherine F. Latham, Nicholas Barlow, George W. Mbogo, Paula Ellenberg, Stephen J. Headey, Nicolas Sluis-Cremer, David Tyssen, Joseph D. Bauman, Francesc X. Ruiz, Eddy Arnold, David K. Chalmers, Gilda Tachedjian
Summary: Human immunodeficiency virus type I (HIV-1) is a major global health burden, and the emergence of drug-resistance mutations necessitates the development of novel drugs. In this study, a fragment-based drug discovery approach was used to optimize a hit fragment (compound B-1) that targets the viral protein reverse transcriptase (RT) in a novel site. Different compound series were synthesized and evaluated for their RT binding and inhibition, leading to the identification of a lead compound with promising inhibitory activity. This study offers a starting point for the development of novel dual inhibitors targeting the NNRTI-binding pocket and an adjacent site.
Article
Biochemistry & Molecular Biology
Jirayu Kammarabutr, Panupong Mahalapbutr, Hisashi Okumura, Peter Wolschann, Thanyada Rungrotmongkol
Summary: This study indicates that certain anti-HIV drugs may have higher susceptibility against HBV-RT enzyme, potentially serving as a promising drug option for HBV-infected patients with 3TC resistance.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Infectious Diseases
Adetayo Emmanuel Obasa, Anoop T. Ambikan, Soham Gupta, Ujjwal Neogi, Graeme Brendon Jacobs
Summary: This study found a significantly higher occurrence of PI RAMs in minor viral quasispecies compared to other types of RAMs in South African patients receiving second-line cART. The detection of certain resistance mutations could be valuable for early identification of acquired resistance.
BMC INFECTIOUS DISEASES
(2021)
Review
Cell Biology
Athanasios-Dimitrios Bakasis, Theodoros Androutsakos
Summary: Since the introduction of ART in 1996, the lifespan of PLWH has increased and the major causes of mortality have shifted towards cardiovascular and liver diseases. HIV itself and various liver diseases may contribute to liver damage and subsequent LF in PLWH. Among ART drug classes, nucleoside reverse transcriptase inhibitors, especially didanosine and zidovudine, appear to pose the greatest risk for LF.
Review
Chemistry, Medicinal
Yuki Yoshida, Masakazu Honma, Yasuaki Kimura, Hiroshi Abe
Summary: Despite the availability of various anti-HIV drugs, NRTIs remain widely used and of interest. However, HIV has developed resistance against NRTIs, necessitating the search for novel therapies to combat the virus.
Article
Biochemistry & Molecular Biology
Kolin M. Clark, Josh G. Kim, Qiankun Wang, Hongbo Gao, Rachel M. Presti, Liang Shan
Summary: The sensitization of the CARD8 inflammasome to non-nucleoside reverse transcriptase inhibitors (NNRTIs) can be achieved through chemical inhibition of the negative regulator DPP9. The DPP9 inhibitor Val-boroPro (VbP) can kill HIV-1-infected cells without NNRTIs and synergize with NNRTIs to promote clearance of infected cells. This offers a promising strategy for enhancing NNRTI efficacy in eliminating HIV-1 reservoirs.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Cell Biology
Carl J. Balibar, Daniel J. Klein, Beata Zamlynny, Tracy L. Diamond, Zhiyu Fang, Carol A. Cheney, Jan Kristoff, Meiqing Lu, Marina Bukhtiyarova, Yangsi Ou, Min Xu, Lei Ba, Steven S. Carroll, Abdellatif El Marrouni, John F. Fay, Ashley Forster, Shih Lin Goh, Meigang Gu, Daniel Krosky, Daniel I. S. Rosenbloom, Payal Sheth, Deping Wang, Guoxin Wu, Matthias Zebisch, Tian Zhao, Paul Zuck, Jay Grobler, Daria J. Hazuda, Bonnie J. Howell, Antonella Converso
Summary: Antiretroviral therapy can inhibit HIV-1 replication but cannot cure the infection due to the persistence of a reservoir in the host genome. Reduction of this reservoir is important for HIV-1 cure. Some nonnucleoside reverse transcriptase inhibitors have shown selective cytotoxicity against HIV-1 in vitro, but their concentrations required are much higher than approved dosages. By focusing on this secondary activity, researchers have discovered bifunctional compounds called targeted activators of cell kill (TACK) that can kill HIV-1-infected cells at clinically achievable concentrations. These TACK molecules bind to the reverse transcriptase-p66 domain of monomeric Gag-Pol and act as allosteric modulators, promoting dimerization and premature intracellular viral protease activation, leading to death of HIV-1(+) cells. TACK molecules retain potent antiviral activity and selectively eliminate infected CD4(+) T cells, providing a potential immune-independent clearance strategy.
SCIENCE TRANSLATIONAL MEDICINE
(2023)
Article
Virology
Duygu Tekin, Deniz Gokengin, Huseyin Onay, Selda Erensoy, Ruchan Sertoz
Summary: The study investigated mutations in PR, RT, and IN gene regions of HIV using NGS, and found NGS to be more sensitive and cost-effective compared to SS. Low-frequency resistance mutations were detected in 18.3% of samples, resulting in virological failure in only one patient. The cost of analysis was reduced by sample pooling and multiplex analysis with the MiSeq system.
JOURNAL OF MEDICAL VIROLOGY
(2021)
Article
Infectious Diseases
Shiyun Lv, Lijun Sun, Tongzeng Li, Ruojing Bai, Man Dai, Ran Wang, Yuanyi Zhai, Wei Hua, Aixin Li, Ruolei Xin, Lili Dai
Summary: This study aimed to analyze the antiretroviral resistance in people living with HIV (PLWH) who developed low-level viremia (LLV) during antiretroviral therapy (ART) by sequencing their HIV-1 proviral DNA and RNA and comparing genotyping data. The results showed moderate concordance between proviral DNA and past/synchronous RNA genotyping, but proviral DNA genotyping provided less information on antiretroviral resistance compared to RNA genotyping. Therefore, a comprehensive evaluation of proviral DNA and RNA genotyping, along with previous treatment history, is essential to optimize ART in PLWH with LLV.
INFECTION AND DRUG RESISTANCE
(2023)
Article
Biochemistry & Molecular Biology
Klarissa Hollander, Albert H. Chan, Kathleen M. Frey, Olivia Hunker, Joseph A. Ippolito, Krasimir A. Spasov, Yang-Hui J. Yeh, William L. Jorgensen, Ya-Chi Ho, Karen S. Anderson
Summary: HIV-1 reverse transcriptase is a key target for HIV drug development. Development of new RT inhibitors, effective against resistant variants, is crucial. Previous drug design efforts have resulted in promising compounds, but their effectiveness against a specific resistance mutation is limited. Crystal structures analysis in this study reveals key features of potent compounds.
Article
Biochemistry & Molecular Biology
Maria Addolorata Bonifacio, Chiara Genchi, Antonella Lagioia, Vincenza Talamo, Anna Volpe, Maria Addolorata Mariggio
Summary: Drug-resistance monitoring is a challenging aspect of HIV management. The evaluation of Vela Diagnostics' NGS platform in Italy showed good performance, with a success rate of 87% and a concordance of 97.2% with Sanger sequencing. The technology demonstrated high accuracy and repeatability.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Wijitra Meelua, Tanchanok Wanjai, Natechanok Thinkumrob, Julianna Olah, Jon Mujika, James R. Ketudat-Cairns, Supa Hannongbua, Jitrayut Jitonnom
Summary: Using QM/MM method, simulations were conducted to understand the dynamics, catalytic mechanism, and electrostatic influence of the active site of GH43 endo-arabinanase, supporting the proposed single-displacement mechanism and identifying potential mutation targets.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Chemistry, Physical
Patchreenart Saparpakorn, Aunlika Chimprasit, Theerawat Jantarat, Supa Hannongbua
Summary: This study investigates the binding of rilpivirine in FIV RT and uses virtual screening to search for new candidates from mushrooms. Cordyceamide A and B from cordyceps were found to be possible to bind with FIV RT, supported by previous reports. Molecular dynamics simulations and quantum chemical calculations confirmed their binding capabilities, with cordyceamide A showing better binding free energies than rilpivirine. The study highlights the potential of these interactions for FIV drug development.
MOLECULAR SIMULATION
(2022)
Article
Biochemistry & Molecular Biology
Siriluk Ratanabunyong, Supaphorn Seetaha, Supa Hannongbua, Saeko Yanaka, Maho Yagi-Utsumi, Koichi Kato, Atchara Paemanee, Kiattawee Choowongkomon
Summary: This research identified the KY44 aptamer as a potential inhibitor of both wildtype and mutant forms of HIV-RT. The aptamer showed low cytotoxicity and inhibited pseudo-HIV particle infection.
Article
Biochemistry & Molecular Biology
Sasipha Seetin, Patchreenart Saparpakorn, Jarunee Vanichtanankul, Danoo Vitsupakorn, Yongyuth Yuthavong, Sumalee Kamchonwongpaisan, Supa Hannongbua
Summary: This study investigated the interactions of a series of compounds with Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) and human DHFR enzymes using various methods. The analysis of key interactions provided a general scheme for designing selective inhibitors for PfDHFR.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Medicinal
Paptawan Thongdee, Chayanin Hanwarinroj, Bongkochawan Pakamwong, Pharit Kamsri, Auradee Punkvang, Jiraporn Leanpolchareanchai, Sombat Ketrat, Patchreenart Saparpakorn, Supa Hannongbua, Kanchiyaphat Ariyachaokun, Khomson Suttisintong, Sanya Sureram, Prasat Kittakoop, Poonpilas Hongmanee, Pitak Santanirand, Galina Mukamolova, Rosemary A. Blood, Yuiko Takebayashi, James Spencer, Adrian J. Mulholland, Pornpan Pungpo
Summary: In this study, virtual screening and biological validation were used to identify candidate inhibitors of Mycobacterium tuberculosis protein kinase B (PknB). Three indole compounds were found to inhibit the growth of M. tuberculosis with minimal inhibitory concentrations. Two compounds also showed inhibition of PknB activity in vitro, while another compound exhibited anti-tuberculosis activity without inhibiting PknB. Molecular dynamics simulations were used to analyze the binding of compounds to PknB, confirming their affinity. These findings provide starting points for the development of new anti-tubercular agents.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Chemistry, Physical
Ratchada Wongkanya, Saranrat Asamo, Decha Dechtrirat, Jutarat Sudchanham, Nirachawadee Srisamran, Chakrit Sriprachuabwong, Adisorn Tuantranont, Nattaporn Chattham, Supa Hannongbua, Pongthep Prajongtat
Summary: A double-step homogeneous precursor mixing process was used to enhance the quality and stability of 2D perovskite precursor solutions, leading to highly stable and efficient solar cells.
ACS APPLIED ENERGY MATERIALS
(2022)
Article
Biochemistry & Molecular Biology
Phujinn Honorio, Supa Hannongbua, Patchreenart Saparpakorn
Summary: This study investigated the key binding interactions of hybrid donepezils for the treatment of Alzheimer's disease (AD) using molecular docking, molecular dynamics simulations, and quantum chemical calculations. The results revealed the important interactions between the hybrid donepezils and key residues in the binding pocket of acetylcholinesterase (AChE). The modification of the scaffolds and HOMO-LUMO predictions provided insights into the electron transfer and adaptation in the binding pocket. The bioavailability, drug-likeness, and pharmacokinetics predictions confirmed the suitability of the hybrid donepezils for AD drug development.
CHEMICO-BIOLOGICAL INTERACTIONS
(2022)
Article
Multidisciplinary Sciences
Wei Lim Chong, Patchareenart Saparpakorn, Chak Sangma, Vannajan Sanghiran Lee, Supa Hannongbua
Summary: The SARS-CoV-2 virus is continuously evolving and mutating, resulting in many of the mutated variants resisting therapeutic monoclonal antibodies (mAbs). Efforts are being made to find mAb with broader neutralization coverage while maintaining neutralizing ability. In this study, the binding affinity of mAb MW06 and its cocktail formulation with MW05 for the SARS-CoV-2 virus receptor binding domain (RBD) was investigated using molecular dynamics simulations (MDs). The combination of MDs and ENM techniques provided simplicity in analyzing the interactions between mAbs and RBD.
Article
Integrative & Complementary Medicine
Viwan Jarerattanachat, Chompunuch Boonarkart, Supa Hannongbua, Prasert Auewarakul, Ruchuta Ardkhean
Summary: This study identified Isoquercitrin, a compound found in Ginseng and Notoginseng, as a potential inhibitor of Dengue NS5 protein. Isoquercitrin showed significant antiviral activity against Dengue virus by reducing viral RNA and protein synthesis with low cell toxicity.
JOURNAL OF TRADITIONAL AND COMPLEMENTARY MEDICINE
(2023)
Article
Chemistry, Medicinal
Bundit Kamsri, Bongkochawan Pakamwong, Paptawan Thongdee, Naruedon Phusi, Pharit Kamsri, Auradee Punkvang, Sombat Ketrat, Patchreenart Saparpakorn, Supa Hannongbua, Jidapa Sangswan, Khomson Suttisintong, Sanya Sureram, Prasat Kittakoop, Poonpilas Hongmanee, Pitak Santanirand, Jiraporn Leanpolchareanchai, Kirsty E. Goudar, James Spencer, Adrian J. Mulholland, Pornpan Pungpo
Summary: Mutations in DNA gyrase confer resistance to fluoroquinolones, second-line antibiotics for Mycobacterium tuberculosis infections. Identification of new agents that inhibit M. tuberculosis DNA gyrase ATPase activity is one strategy to overcome this. Compound R3-13, derived from bioisosteric designs, is a promising ATPase inhibitor against M. tuberculosis DNA gyrase. Additional screening using R3-13 as a template identified seven more ATPase inhibitors, with compound 1 showing the highest potency and noncytotoxicity to Caco-2 cells. Molecular dynamics simulations suggest that compound 1 binds to the ATP binding pocket in M. tuberculosis DNA gyrase GyrB subunit, making it a potential scaffold for further optimization.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Biochemistry & Molecular Biology
Pavinee Prapassornwattana, Supa Hannongbua, Patchreenart Saparpakorn
Summary: This study reported the inhibitory activity of a benzene sulfonamide derivative against Coxsackievirus B3. By using molecular dynamics simulations and density functional theory, the key interactions between the compound and the viral capsid were investigated, and the differences in inhibitory activity against different mutants were explained. These findings are important for the development of drugs against CVB3.
BIOPHYSICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Supaphorn Seetaha, Nuntaporn Kamonsutthipaijit, Maho Yagi-Utsumi, Yanaka Seako, Takumi Yamaguchi, Supa Hannongbua, Koichi Kato, Kiattawee Choowongkomon
Summary: This study characterized the structure and monomer forms of HIV-1 RT using biophysical techniques, and found that the unliganded monomers have different conformations compared to the complexes. Small-angle X-ray scattering experiments confirmed the binding of p66(W401A) and p51(W401A) with inhibitors.
Article
Chemistry, Multidisciplinary
Kewalin Posansee, Monrudee Liangruksa, Teerasit Termsaithong, Patchreenart Saparpakorn, Supa Hannongbua, Teeraphan Laomettachit, Thana Sutthibutpong
Summary: A deep learning model supported by principal component analysis and structural methods was used to search for an alternative mTOR inhibitor from mushrooms. Through filtering and molecular docking calculations, a potential candidate with therapeutic value was identified.
Article
Biochemical Research Methods
Malinee Promkatkaew, Pornthip Boonsri, Songwut Suramitr, Thitinun Karpkird, Peter Wolschann, Supa Hannongbua
Summary: This study investigated the host-guest interaction between methoxy cinnamic acid derivatives and cyclodextrins using density functional theory (DFT) and timedependent DFT (TD-DFT) calculations. The results revealed that intermolecular hydrogen bonds are the main driving force of this interaction. In addition, UV-vis absorption spectra analysis showed that one particular orientation is the most stable and similar to the parent MCA in terms of absorption in both UVB and UVA regions. These findings provide valuable insights into the host-guest interaction and stability improvement of UV-filter compounds.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2023)
Article
Pharmacology & Pharmacy
Suriyan Thengyai, Yuewei Guo, Khanit Suwanborirux, Heinz Berner, Helmut Spreitzer, Peter Wolschann, Supa Hannongbua, Anuchit Plubrukarn
Summary: A series of scalarane sesterterpenes were synthesized using heteronemin (1) as the primary precursor. QSAR models based on 2D-QSAR and CoMFA approaches were built using a total of 22 antitubercular scalaranes obtained from natural sources and synthesis. The models indicated the significance of substitutions near C-12 and C-16 of the scalaranes.
SCIENTIA PHARMACEUTICA
(2022)
Article
Biochemical Research Methods
Nousheen Parvaiz, Asma Abro, Syed Sikander Azam
Summary: Protein Tyrosine Phosphatase 1B (PTP1B) is a negative regulator of insulin signaling pathways and has potential as a medicinal target. This study explores the binding and conformational orientation of zinc(II) complexes in PTP1B using advanced computational methods. The findings suggest that zinc(II) complexes can bind to important residues in the enzyme and inhibit its activity.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Hira Zubair, Muhamed Salim Akhter, Muhammad Waqas, Mariam Ishtiaq, Ijaz Ahmed Bhatti, Javed Iqbal, Ahmed M. Skawky, Rasheed Ahmad Khera
Summary: Improving open-circuit voltage is crucial for enhancing the overall efficiency of organic solar cells. This study successfully improved the open-circuit voltage by modulating the molecular structure and proposed a promising design concept for acceptor molecules that may contribute to the development of advanced organic solar cells.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Jerica Wilson, Bahrad A. Sokhansanj, Wei Chuen Chong, Rohan Chandraghatgi, Gail L. Rosen, Hai-Feng Ji
Summary: Fragment-based drug design is a computer-aided drug discovery method, however, it has limitations in processing time and success rate. In this study, a new method called Fragment Databases from Screened Ligands Drug Design (FDSL-DD) was proposed, which intelligently incorporates fragment characteristics into the drug design process to improve the binding affinity between drugs and protein targets.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
M. Chamani, G. H. Farrahi
Summary: This paper employs the Generalized Particle (GP) method to simulate nanoindentation and nanoscratching, showing that this method maintains consistent atomic properties across different scales and achieves results consistent with full atomic simulations.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Paola Vottero, Elena Carlotta Olivetti, Lucia Chiara D'Agostino, Luca Di Grazia, Enrico Vezzetti, Maral Aminpour, Jacek Adam Tuszynski, Federica Marcolin
Summary: This study aims to characterize the spike protein of the SARS-CoV-2 virus and investigate its interaction with the ACE2 receptor using a geometric analysis. The 3D depth maps of the proteins are filtered using a specific convolutional filter to obtain geometric features. Geometric descriptors and a Support Vector Machine classifier are used for feature extraction and classification, revealing the geometrical reasons for the higher contagiousness of the Omicron variant compared to other variants.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Diana Margarita Mojica-Munoz, Karla Lizbeth Macias-Sanchez, Estefania Odemaris Juarez-Hernandez, Aurora Rodriguez-Alvarez, Jean-Michel Grevy, Armando Diaz-Valle, Mauricio Carrillo-Tripp, Jose Marcos Falcon-Gonzalez
Summary: By employing molecular dynamics simulations, we investigated the molecular mechanisms underlying the plasticization of starch. Our study revealed that chain size affects the solubility of starch, temperature influences its diffusivity and elastic properties, and oleic acid shows potential as an alternative plasticizer. Blending glycerol or oleic acid with water enhances the elasticity of starch.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Sandip Kumar Baidya, Suvankar Banerjee, Balaram Ghosh, Tarun Jha, Nilanjan Adhikari
Summary: This study utilized classification-based QSAR techniques and fragment-based data mining to analyze different MMP-9 inhibitors, revealing the importance of certain molecular fragments in MMP-9 inhibition. These findings have implications for the development of effective MMP-9 inhibitors in the future.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Farid Faraji Chanzab, Saber Mohammadi, Fatemeh Alemi Mahmoudi
Summary: A comprehensive study using molecular dynamics technique was conducted to investigate the behavior of PAP molecules in a n-heptane/toluene solution and the role of SWCNTs, both bare and functionalized with carboxyl groups, in the aggregation of PAP molecules. The study found that the CNTs hindered the association of PAP molecules through steric hindrance and adsorption mechanisms. The presence of carboxyl groups on the CNTs improved the stability and adsorption of PAP molecules. The results have implications for future research on controlling asphaltene precipitation in the oil industry.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Ramin Bairami Habashi, Mohammad Najafi, Reza Zarghami
Summary: A vigorous Monte Carlo strategy was developed to simulate the copolymerization of ethylene and 1-butene using a dual-site metallocene catalyst. The results showed that the second catalyst site had higher activity than the first site, with ethylene and 1-butene consumption rates five times higher and hydrogen transfer rates three times faster. The molar percentage of 1-butene in the copolymers synthesized from the second site was around 12%, while in the copolymers from the first site it was around 2%. Increasing the 1-butene concentration led to an increase in overall molecular weight, while increasing the hydrogen concentration resulted in a decrease in molecular weight. The ratio of ethylene to 1-butene affected the melt index and the weight fraction of crystals, with higher ratios leading to smaller melt indexes and higher weight fractions of crystals. Increasing the temperature caused changes in molecular weight, bimodal molecular weight distribution, crystal thickness and weight fraction, and density of HDPE.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Yufan Lu, Xingmin Guo, Shuya Liu
Summary: This paper investigates how to control the nontrivial topological structures of DNA nanocages by adjusting the number of ssDNA strands. A new algorithm and program are developed to calculate the component number of polyhedral links, filling the gap in computer programs on this aspect. The study provides a complete list of topological structures with different component numbers for DNA octahedrons assembled from one or more ssDNA strands.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Peng Cui, Shideng Yuan, Heng Zhang, Shiling Yuan
Summary: Understanding the mechanisms of viscosity enhancement in crude oil phases is crucial for optimizing extraction and transportation processes. This study employed molecular dynamics simulations to investigate the behavior and viscosification mechanism of asphaltene molecules in complex oil phases. The research suggests that electrostatic interactions and interactions between asphaltene and crude oil molecules contribute to the enhanced viscosity. The findings provide insight into the viscosity enhancement mechanisms in crude oil phases.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Kun Lv, Jin Zhang, Xiaohua Liu, Yuqiao Zhou, Kai Liu
Summary: In this paper, the authors propose a robust method for evaluating the interactions between chiral catalysts and substrates using computer simulations. The method involves constructing 3D models from point cloud data, filtering out non-interacting points, determining interacting points, and accurately calculating interacted volumes. Experimental results demonstrate the effectiveness of the method in removing non-interacting points and calculating interacted volumes with low errors.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Crisciele Fontana, Joao Luiz de Meirelles, Hugo Verli
Summary: By using the GROMOS force field and molecular simulations, this study assessed the dynamics of STA-analogs in aqueous solution and their interaction with water, expanding the knowledge of the conformational space of these ligands and providing potential implications for understanding conformational selection during complexation.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Wei Zhao, Wenjie Zou, Fengyang Liu, Fang Zhou, N. Emre Altun
Summary: The effect of grafting rate on the water solubility of chitosan-grafted polyacrylamide (Chi-gPAM) was investigated using molecular dynamics simulations. The results showed that the intramolecular hydrogen bonding of Chi-gPAM played a dominant role in its water solubility. Additionally, the interaction between Chi-gPAM and water increased with grafting rate.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Nassima Bachir, Samir Kenouche, Jorge I. Martinez-Araya
Summary: This study investigates the local chemical reactivity of FOX-7 and explores the interaction between the compound and different metals. The findings suggest that the stability and charge transfers of the compound are influenced by the metal involved, and the interaction between Metallocene Methyl Cations and the compound shows potential for neutralization.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)