Article
Biochemistry & Molecular Biology
Sofia D'Souza, S. Balaji, K. Prema
Summary: This study successfully developed new 3CL protease inhibitors using 2D and 3D QSAR models, and validated their inhibitory effects on SARS-CoV through molecular docking and molecular dynamics simulations. The newly designed compounds showed higher interaction energies with active site residues and improved pharmacokinetic properties.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Konda Mani Saravanan, Haiping Zhang, Renganathan Senthil, Kevin Kumar Vijayakumar, Vignesh Sounderrajan, Yanjie Wei, Harshavardhan Shakila
Summary: A novel coronavirus outbreak has posed a severe threat to human healthcare globally, and researchers have been searching for ways to control and prevent this deadly disease. In this study, antiviral compounds from traditional Indian medicinal plants were screened, and amentoflavone was identified as a potential inhibitor of the SARS-CoV2 main protease. Further biochemical experiments are needed to understand the mechanism of inhibition by these plant-derived antiviral compounds.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Suwicha Patnin, Arthit Makarasen, Pongsit Vijitphan, Apisara Baicharoen, Apinya Chaivisuthangkura, Mayuso Kuno, Supanna Techasakul
Summary: In this study, the binding interactions of phenylamino-phenoxy-quinoline derivatives and SARS-CoV-2 main protease (M-pro) were investigated, and two compounds were found to have low binding energy values and appropriate molecular properties for binding to M-pro via hydrogen bonding and Pi-Pi stacking interactions.
Article
Chemistry, Medicinal
Piyatida Pojtanadithee, Kowit Hengphasatporn, Aphinya Suroengrit, Siwaporn Boonyasuppayakorn, Patcharin Wilasluck, Peerapon Deetanya, Kittikhun Wangkanont, I. Putu Sukanadi, Warinthorn Chavasiri, Peter Wolschann, Thierry Langer, Yasuteru Shigeta, Phornphimon Maitarad, Kamonpan Sanachai, Thanyada Rungrotmongkol
Summary: SWC423, a sulfonamide chalcone, has been identified as a potential inhibitor of the 3CL(pro) enzyme and shows promising antiviral activity against SARS-CoV-2. Its competitive inhibition and low cytotoxicity make it a suitable candidate for further research on COVID-19 treatment development.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Multidisciplinary Sciences
Asim Kumar Bepari, Hasan Mahmud Reza
Summary: This study used a comprehensive computational approach to screen inhibitors for the SARS-CoV-2 main protease, offering a potential lead for antiviral drug discovery against COVID-19.
Article
Biology
Mohsen Sisakht, Aida Solhjoo, Amir Mahmoodzadeh, Mohammad Fathalipour, Maryam Kabiri, Amirhossein Sakhteman
Summary: The study explores the potential application of NSAIDs as antiviral drugs against COVID-19, suggesting that certain NSAIDs may inhibit the main protease, and evaluates their hepatotoxicity using systems biology techniques.
COMPUTERS IN BIOLOGY AND MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Mohit Motiwale, Neetu Singh Yadav, Sushil Kumar, Tushar Kushwaha, Gourav Choudhir, Supriya Sharma, Pradeep Kumar Singour
Summary: In this study, computer-aided drug design techniques were used to identify potential inhibitors with anti-viral activity against SARS-CoV-2. The results showed that N-substituted isatin derivatives and pyrazolone compounds could be effective inhibitors. However, further experimental investigation and validation are needed to determine their suitability for clinical trials.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Chemistry, Medicinal
Lucile Brier, Haitham Hassan, Xavier Hanoulle, Valerie Landry, Danai Moschidi, Lowiese Desmarets, Yves Rouille, Julie Dumont, Adrien Herledan, Sandrine Warenghem, Catherine Piveteau, Paul Carr, Sarah Ikherbane, Francois-Xavier Cantrelle, Elian Dupre, Jean Dubuisson, Sandrine Belouzard, Florence Leroux, Benoit Deprez, Julie Charton
Summary: Since the end of 2019, the global outbreak of the coronavirus SARS-CoV-2 has caused a significant increase in infections and deaths worldwide. Researchers have identified two proteases, 3CLpro and papain-like protease, encoded by the virus that play a crucial role in the virus lifecycle. Targeting the 3CLpro, which is highly conserved within this viral family, a screening of over 89,000 small molecules led to the discovery of a potent inhibitor of the SARS-CoV-2 3CLpro. The mechanism of inhibition, interaction with the protease, specificity against host proteases, and promising antiviral properties in cells are reported.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Venkatramanan Varadharajan, Gokulakrishnan Sivasundari Arumugam, Sethupathi Shanmugam
Summary: This study screened potential SARS-CoV-2 Mpro inhibitors from existing literature on isatin derivatives, ultimately selecting 4 compounds with good ADMET properties and binding energies as lead candidates for further experimental validation and development.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Chemistry, Physical
Shipra Bhati, Vikas Kaushik, Joginder Singh
Summary: This study designed a series of inhibitors targeting SARS-CoV 3CL protease with potential anti-COVID-19 infection effects.
JOURNAL OF MOLECULAR STRUCTURE
(2021)
Article
Virology
Sophakama Zabo, Kevin Alan Lobb
Summary: The main protease (M-pro) of SARS-CoV-2 is crucial for the virus's life cycle. It cleaves the polyproteins to form mature proteins, essential for virion formation. Molecular docking and molecular dynamics simulations were performed to study the recognition and cleavage of hexapeptides by M-pro. The results provided insights into M-pro's substrate recognition and its implications for developing small molecule inhibitors.
Article
Chemistry, Physical
Assia Belhassan, Samir Chtita, Hanane Zaki, Marwa Alaqarbeh, Nada Alsakhen, Firas Almohtaseb, Tahar Lakhlifi, Mohammed Bouachrine
Summary: COVID-19 is a new infectious disease caused by the SARS-CoV-2 virus, and finding drugs for its treatment is an important requirement. The study suggests that Riboflavin (Vitamin B2) could be of interest for the antiviral treatment of COVID-19.
JOURNAL OF MOLECULAR STRUCTURE
(2022)
Article
Biochemistry & Molecular Biology
Sakshi Piplani, Puneet Singh, Nikolai Petrovsky, David A. Winkler
Summary: The urgent need for drugs to treat COVID-19 has led to a search for existing drugs and natural compounds that can be repurposed quickly. Researchers have developed a fast and robust computational process to screen large libraries of compounds, identifying potential inhibitors of the main protease of SARS-CoV-2. The top candidate compounds show promising activity against COVID-19 and provide leads for further experimental validation.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Chemistry, Physical
Temitope Isaac Adelusi, Abdul-Quddus Kehinde Oyedele, Ojo Emmanuel Monday, Ibrahim Damilare Boyenle, Mukhtar Oluwaseun Idris, Abdeen Tunde Ogunlana, Ashiru Mojeed Ayoola, John Olabode Fatoki, Oladipo Elijah Kolawole, Kehinde Busuyi David, Akintola Adebola Olayemi
Summary: The study investigated the inhibitory potential of fifty dietary polyphenols against the main protease of the SARS-like Coronavirus. Among them, Ellagic acid, Kievitone, and Punicalin showed promising binding affinities, while further analysis suggested punicalin may have adverse effects in clinical trials.
JOURNAL OF MOLECULAR STRUCTURE
(2022)
Review
Pharmacology & Pharmacy
Anirban Mandal, Ajeet Kumar Jha, Banasri Hazra
Summary: The ongoing COVID-19 pandemic poses a significant global health security threat with no specific treatment available. Research has shown that compounds from medicinal plants exhibit strong activity in inhibiting coronavirus 3CL protease, offering potential for the development of new drugs against COVID-19.
FRONTIERS IN PHARMACOLOGY
(2021)
Article
Biochemical Research Methods
Marina Macchiagodena, Marco Pagliai, Piero Procacci
Summary: The study examined the non-covalent interaction between PF-07321332 and the SARS-CoV-2 main protease using computational methods. It found that the binding is likely to be stronger when the catalytic dyad is in a neutral state.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2022)
Article
Chemistry, Physical
Piero Procacci, Guido Guarnieri
Summary: In this paper, blind predictions for the binding of WP6 with ammonium/diammonium cationic guests in the ninth challenge of SAMPL are presented. The binding free energies were calculated using a virtual double system single box approach and compared with previous submissions. The results show acceptable performance with higher accuracy than previous challenges, indicating the reliability of nonequilibrium approaches for binding free energy calculations.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Piero Procacci
Summary: In the field of drug design, a dual topology alchemical approach for calculating binding free energy between different compounds is proposed. This method overcomes the limitations of traditional single topology methods and has been validated in various test scenarios. It is specifically designed for high-performance computing facilities and can be easily implemented in popular simulation software.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Multidisciplinary
Marina Macchiagodena, Marco Pagliai, Piero Procacci
Summary: We present a step-by-step protocol and toolkit for calculating the relative dissociation free energy (RDFE) using the GROMACS molecular dynamics package. This approach, based on a novel bidirectional nonequilibrium alchemical method, accurately computes RDFE between small molecules with different volume, charge, and chemical topology. The methodology is demonstrated using the challenging SAMPL9 batch of host-guest pairs. The article is supported by an online tutorial and a public Zenodo repository.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2023)
Article
Chemistry, Physical
Marina Macchiagodena, Gavino Bassu, Irene Vettori, Emiliano Fratini, Piero Procacci, Marco Pagliai
Summary: This study investigates the structural properties of 2-butanol aqueous solutions at different concentrations using both experimental and computational methods. It has been found that 2-butanol tends to form aggregates at concentrations above 1 M, which affects the structural and dynamic properties of the solvent.
JOURNAL OF PHYSICAL CHEMISTRY A
(2022)
Article
Chemistry, Multidisciplinary
Margherita Verrucchi, Gina Elena Giacomazzo, Patrick Severin Sfragano, Serena Laschi, Luca Conti, Marco Pagliai, Cristina Gellini, Marilena Ricci, Enrico Ravera, Barbara Valtancoli, Claudia Giorgi, Ilaria Palchetti
Summary: A water-soluble ruthenium(II) complex (L) was used to modify the surface of an indium-tin oxide (ITO) electrode decorated with a nanostructured layer of TiO2 (TiO2/ITO). Singlet oxygen (O-1(2)) produced by the complex under visible light irradiation triggers a cathodic photocurrent when the electrode is illuminated and biased at a proper reduction potential. The L/TiO2/ITO electrode was characterized and demonstrated efficient oxidation of phenolic compounds, with a limit of detection (LOD) of 0.3 mu mol dm(-3).
Article
Biochemistry & Molecular Biology
Milana Bazayeva, Andrea Giachetti, Marco Pagliai, Antonio Rosato
Summary: Classical molecular dynamics (MD) simulations are commonly used to study the behavior of zinc(II)-proteins at the atomic level. In this study, the accuracy of two force fields (ZAFF and NBFF) in reproducing the dynamic behavior of zinc(II)-proteins was assessed using six zinc-fingers as benchmark. The results indicated that both force fields can accurately reproduce protein dynamics with comparable accuracy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Physical
Piero Procacci, Guido Guarnieri
Summary: We describe our blind prediction of the toluene-water partition coefficients in the SAMPL9 challenge. We used an efficient MD-based nonequilibrium alchemical technique relying on the GAFF2 non-polarizable force field. The prediction was optimized based on a pre-assessment comparing with known experimental data and provides valuable insights for improving the performance of the force field in drug-receptor system calculations.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Biochemistry & Molecular Biology
Michele Casoria, Marina Macchiagodena, Paolo Rovero, Claudia Andreini, Anna Maria Papini, Gianni Cardini, Marco Pagliai
Summary: The standard GAFF2 force field parameterization has been refined for three fluorinated alcohols commonly used to study proteins and peptides in biomimetic media. The newly proposed models are validated through experimental findings, supporting their accuracy and effectiveness.
JOURNAL OF PEPTIDE SCIENCE
(2023)
Article
Chemistry, Physical
Piero Procacci
Summary: This study tested the performance of standard molecular dynamics (MD) simulations, replicates of shorter MD simulations, and Hamiltonian Replica Exchange (HREM) simulations for sampling in two macrocyclic hosts and a drug-receptor system. The results showed that enhanced sampling techniques were necessary for reliable sampling in the macrocycle with long-lived metastable states.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Meeting Abstract
Biochemistry & Molecular Biology
Michele Casoria, Paolo Rovero, Anna Maria Papini, Gianni Cardini, Marina Macchiagodena, Claudia Andreini, Marco Pagliai
JOURNAL OF PEPTIDE SCIENCE
(2022)
Article
Chemistry, Physical
Jonathan Campeggio, Victor Volkov, Massimo Innocenti, Walter Giurlani, Claudio Fontanesi, Mirco Zerbetto, Marco Pagliai, Alessandro Lavacchi, Riccardo Chelli
Summary: This study focuses on the first step of the ethanol electro-oxidation catalyzed by Pd in an alkaline environment, which is the hydrogen atom abstraction. Quantum and molecular mechanics calculations reveal that the solvent significantly affects the adsorption free energies of ethanol and hydroxyl ions, leading to a decrease in their adsorption energy. Furthermore, it is observed that hydrogen atom abstraction is enhanced when the reactants weakly interact with the catalyst. The study suggests that the catalytic coverage of Pd in an aqueous environment is mainly dominated by OH rather than ethanol, and only a small fraction of weakly bound reactants are truly active in the ethanol electro-oxidation reaction.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Correction
Chemistry, Physical
Chen Luo, Yan Shao, Hua Yu, Hong-zhi Ma, Yu-hao Zhang, Long Gu, Bo Yin, Ming-bo Yang
CHEMICAL PHYSICS LETTERS
(2024)
Article
Chemistry, Physical
Stefano Borocci, Armando Camerlingo, Felice Grandinetti, Maria Rutigliano, Nico Sanna
Summary: The complexes of He, Ne, Ar, Kr, and Xe with B3N3H6 were investigated using MP2, CCSD(T), and SAPT ab initio methods. The complexes can be described as mono-, di-, and tri-coordinated to the N atoms, with stability following the order N-mono < N-di < N-tri. The interactions are dominated by dispersion and the binding energies are within the range of 1 or 2 kcal mol(-1). The results were compared with a recent DFT study on larger BN sheets complexes [Phys. Chem. Chem. Phys. 24 (2022) 2554-2566.].
CHEMICAL PHYSICS LETTERS
(2024)
Article
Chemistry, Physical
V. Nagarajan, R. Bhuvaneswari, R. Chandiramouli
Summary: In this study, stable phosphoborane was used as a sensor to detect isobutane and n-propane in Liquefied Petroleum Gas (LPG). Phosphoborane demonstrated structural stability and semiconducting nature, and exhibited promising adsorption properties for the LPG molecules.
CHEMICAL PHYSICS LETTERS
(2024)
Article
Chemistry, Physical
Xiaoxi Xu, Zijiang Yang, Bayaer Buren, Maodu Chen
Summary: In this study, the time-dependent wave packet method was used to investigate the reaction channels and mechanisms of Ca+ + HD. The results show that the CaH+ + D reaction channel plays a primary role, which is consistent with experimental results. Complex forming and direct-abstraction reaction mechanisms exist in this reaction process.
CHEMICAL PHYSICS LETTERS
(2024)
Article
Chemistry, Physical
Keshab Pandey, Hae Kyung Jeong
Summary: A free-standing silicon-carbon nanofiber composite film was synthesized and investigated for supercapacitor applications. It exhibited high specific capacitance, energy density, and power density. After 5000 cycles, the film showed excellent specific capacitance retention and Coulombic efficiency.
CHEMICAL PHYSICS LETTERS
(2024)
Article
Chemistry, Physical
Xinyu Zhang, Haosong Li, Xiaoyu Cao, Jing Gao, Yong Wei, Jianzhuo Zhu
Summary: The evaporation behavior of nanosized water aggregations on two-dimensional electroneutral solid surfaces with different surface polar unit densities was investigated. The results showed that the evaporation rate changes non-monotonically with the surface polar unit density, and the minimum evaporation rate is obtained when the surface has a modest surface polar unit ratio of 66.7%.
CHEMICAL PHYSICS LETTERS
(2024)
Article
Chemistry, Physical
Yanyan Xu, Rui Dai, Xiaojie Wang, Zhijun Qiao, Haowei Wen, Dianbo Ruan, Yuzuo Wang
Summary: This article presents an innovative solvothermal sodium insertion method for synthesizing Triphylite-NaFePO4, which demonstrates optimal electrochemical performance in sodium-ion batteries.
CHEMICAL PHYSICS LETTERS
(2024)
Article
Chemistry, Physical
Meiyi Jiang, Kun Yang, Yancheng Liu, Li Yao
Summary: The geometric structure and electronic properties of transition metal M (M = Cu, Fe, Mn)-TiO2 (101) surface adsorbed by NO2 and N2O were calculated by density functional theory (DFT) and DFT + U theory. The results showed that the adsorption of NO2 and N2O on Mn and Fe atoms is more stable, and a large number of active electrons are formed around these atoms, facilitating the catalytic reactions.
CHEMICAL PHYSICS LETTERS
(2024)
Article
Chemistry, Physical
Sergey A. Vyrko, Yulia G. Polynskaya, Nikita A. Matsokin, Andrey M. Popov, Andrey A. Knizhnik, Nikolai A. Poklonski, Yurii E. Lozovik
Summary: In this study, carbon nanobracelets, which are cyclic molecules composed of alternating polycyclic regions and double carbon chains, were investigated using spin-polarized density functional theory. The results show that carbon nanobracelets with odd number of monomers exhibit distinct electronic energy levels, band gaps, and carbon chain deformation compared to those with even number of monomers.
CHEMICAL PHYSICS LETTERS
(2024)
Article
Chemistry, Physical
Chanchan Wang, Quan Yang, Yanzhi Ding, Xiaoyong Lu, Dong Tian
Summary: It has been found that the introduction of buffer layers improves the electrical performance of solid oxide fuel cells (SSOFCs). In this study, varying ratios of Gd-doped CeO2 were used as buffer layers in YSZ-based SSOFCs. The results demonstrate that the performance of SSOFCs is enhanced when a buffer layer is added, with the highest performance achieved using Ce0.8Gd0.2O2-delta (GDC20) as the buffer layer. This suggests that the use of GDC series buffer layers is an attractive strategy to optimize performance loss due to electrolyte-electrode interactions.
CHEMICAL PHYSICS LETTERS
(2024)
Article
Chemistry, Physical
Wang Li, Yi-Fan Zhang, Jia-Bin Huang, Chang-Yang Wang, Feng Zhang, Jiu-Zhong Yang, Long Zhao
Summary: The gas-phase reaction of propargyl with vinylacetylene was investigated using synchrotron photoionization and molecular-beam mass spectrometry methodologies. The formation mechanisms of the resulting cyclic structures were examined using quantum computations. Two previously unidentified isomers were detected and identified for the first time.
CHEMICAL PHYSICS LETTERS
(2024)
Article
Chemistry, Physical
Avijit Pramanik, Sanchita Kundu, Olorunsola Praise Kolawole, Kaelin Gates, Paresh Chandra Ray
Summary: This study investigates the influence of aspect ratio and quantum confinement on the single-photon and two-photon absorption cross-section of perovskite CsPbI3 nanorods. Experimental data shows that CsPbI3 nanorods have an extremely high two-photon absorption cross-section, significantly surpassing organic chromophores and other CsPbBr3 nanocrystals. Moreover, adjusting the aspect ratio can significantly enhance the absorption ability. Additionally, the study also reveals a moderate quantum confinement effect on the single-photon and two-photon absorption cross-section of the nanorods.
CHEMICAL PHYSICS LETTERS
(2024)
Article
Chemistry, Physical
Hyon-Tae Pak, Jin-A Choe, Kyong-Sik Ju, Yong -Son Rim
Summary: Drug-loaded cellulose diacetate (CDA) membranes were prepared using different compositions of mixed solvent. The microstructure and performance of the membranes were investigated, and a method to predict drug release properties was proposed. The results showed that the composition of the mixed solvent significantly affected the overall performance of CDA membranes, and the release rates of drugs were related to Δdelta and the intrinsic viscosity of CDA.
CHEMICAL PHYSICS LETTERS
(2024)
Article
Chemistry, Physical
Gabriella E. Ravin, E. Curotto
Summary: We have developed a systematic approach to optimize the training set sizes for neural networks in fitting ab initio potential energy surfaces. Using this approach, we have constructed several spectroscopic quality potential energy surfaces for [Li(H2)n]+, n = 1 - 9. The ground state properties have been computed for all the systems and selected states.
CHEMICAL PHYSICS LETTERS
(2024)
Article
Chemistry, Physical
Guohua Xu, Lei Xu, Feng Zhang, Chunling Yu, Yu Song
Summary: NiS1.03@Ni7S6/carbon composite was successfully prepared using corn stalk as a carbon source via a simple adsorption-sulphurization process. The composite exhibited a specific capacitance of 1554.6 F/g at 1 A/g as a supercapacitor electrode, with a capacitance retention rate of 80.4% after 5000 cycles. Furthermore, the NiS1.03@Ni7S6/carbon//AC asymmetric supercapacitor showed a high energy density of 41.2 Wh kg-1 at a power density of 750 W kg-1, and excellent cycling stability with 86.8% capacitance retention after 10,000 cycles.
CHEMICAL PHYSICS LETTERS
(2024)