Article
Chemistry, Multidisciplinary
Zackary Falls, Jonathan Fine, Gaurav Chopra, Ram Samudrala
Summary: The study evaluated a novel molecular docking protocol CANDOCK and demonstrated its superiority in predicting inhibitor potency to the HIV-1 protease. Experimental results showed that CANDOCK performed better than Autodock Vina and Smina in predicting binding scores and discriminating active versus decoy ligands.
FRONTIERS IN CHEMISTRY
(2022)
Article
Chemistry, Medicinal
Georgios Iakovou, Stephen D. Laycock, Steven Hayward
Summary: Interactive docking allows users to guide and control the docking of biomolecules, beneficial for SBDD and educating students on biomolecular interactions. It introduces DockIT for VR, which models conformational changes within the receptor in real-time.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Biochemistry & Molecular Biology
Roberto Arrigoni, Luigi Santacroce, Andrea Ballini, Luigi Leonardo Palese
Summary: The availability of drugs capable of blocking microorganism replication is a major accomplishment in medicine, but the increasing number of resistant strains poses a significant challenge for infectious disease treatment. Therefore, the search for new potential ligands for pathogens' life cycle is a crucial research area today.
Article
Biochemistry & Molecular Biology
Gabriele La Monica, Antonino Lauria, Alessia Bono, Annamaria Martorana
Summary: The approval of HIV-1 protease inhibitors marked an important step in AIDS treatment, but also led to severe side effects. In-silico techniques can help design new selective inhibitors with well-fitting selectivity and without undesirable interactions. This new method could be a reliable tool in the research of targeted small molecules.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemical Research Methods
Suchetana Gupta, Sangeetha Balasubramanian, Sanjib Senapati
Summary: HIV-1 protease is a key enzyme in the virus lifecycle, and inhibiting its dimerization can help inhibit virus replication; Novel therapeutic approaches are under exploration, including synthetic antibodies; The study indicates strong interactions between mAB and key residues of PR, providing a basis for designing allosteric inhibitors preventing HIV-1 protease dimerization.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2021)
Article
Biochemistry & Molecular Biology
Bowen Pan, Sumei Li, Junwei Xiao, Xin Yang, Shouxia Xie, Ying Zhou, Jian Yang, Ying Wei
Summary: This study screened potential antiviral compounds from Sarcandra glabra and investigated their inhibitory effects on HIV-1 and Cathepsin L proteases. The results showed that the extracts from Sarcandra glabra inhibited both proteases, with chlorogenic acid identified as the most potent inhibitor. These findings suggest that Sarcandra glabra extracts and its active ingredients may have dual-inhibition functions against viral proteases and could be used for preventing or treating viral infections, including SARS-CoV-2.
Article
Biochemistry & Molecular Biology
Sunday N. Okafor, Pavimol Angsantikul, Hashim Ahmed
Summary: This research utilized computational tools to screen a large compound library and identified potential HIV-1 protease inhibitors. Two optimized molecules showed promising activity and should be further investigated in vitro and in clinical trials.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Shanshan Wu, Huiyu Li, Ao Ma
Summary: The primary goal of protein science is to understand the functional mechanisms of proteins and their transitions between different functional structures. However, identifying the exact reaction coordinates in complex molecules remains challenging. In this study, the researchers used a generalized work functional to discover the exact reaction coordinates for the flap opening of HIV-1 protease, providing a precise definition of collectivity and cooperativity in protein dynamics.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Priyashi Rao, Dweipayan Goswami, Rakesh M. Rawal
Summary: The study revealed that curcumin induces mortality in Cx. pipiens at an early stage of its life cycle by inhibiting AChE, showing high biochemical efficacy. This research highlights the potential of curcumin as an emerging natural product insecticide.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Shangjiu Hu, Ling Ma, Biao Dong, Qi Shan, Jinming Zhou, Guoning Zhang, Minghua Wang, Shan Cen, Mei Zhu, Juxian Wang, Yucheng Wang
Summary: A new class of HIV-1 protease inhibitors with phenol derived P2 ligands and nitro or halogens in P2' ligands have been designed and synthesized. Compound 17d displays potent enzyme inhibitory activity and greater antiviral activity against the DRV-resistant variant than the wild type virus.
BIOORGANIC & MEDICINAL CHEMISTRY
(2022)
Article
Chemistry, Medicinal
Bo Wen Pan, Jun Wei Xiao, Su Mei Li, Xin Yang, Xia Zhou, Qing Wen Sun, Mei Chen, Shou Xia Xie, Meena Kishore Sakharkar, Jian Yang, Ying Zhou, Ying Wei
Summary: In this study, the antiviral activities of extracts from the insect gall of Hypericum kouytchense were evaluated. The active ingredients were identified and quantified, and their interactions with proteases were analyzed using molecular docking. The results suggest that these extracts and active ingredients have the potential to be developed for preventing and treating HIV or SARS-CoV-2 infections.
Article
Virology
David Ferreiro, Ruqaiya Khalil, Maria J. Gallego, Nuno S. Osorio, Miguel Arenas
Summary: This study investigates the stability evolution of the human immunodeficiency virus (HIV-1) protease (PR) and finds that the PR has a wide structural plasticity to accommodate mutations without affecting overall stability evolution.
Article
Chemistry, Physical
K. Parveen Begaum, T. Prabhu, S. Kaleeswaran, Shine Kadaikunnan, Ghulam Abbas, S. Muthu, Irem Kestek, Aysen Alaman Agar, Emine Berrin Poyraz, Necmi Dege
Summary: In this study, a Schiff base compound was successfully synthesized and characterized, and its properties were comprehensively investigated using computational methods. The results of vibrational analysis and theoretical calculations were in good agreement with experimental data. Furthermore, the compound showed potential pharmaceutical properties.
JOURNAL OF MOLECULAR STRUCTURE
(2023)
Article
Chemistry, Medicinal
Timofey V. Losev, Igor S. Gerasimov, Maria V. Panova, Alexey A. Lisov, Yana R. Abdyusheva, Polina V. Rusina, Eugenia Zaletskaya, Oleg V. Stroganov, Michael G. Medvedev, Fedor N. Novikov
Summary: Bioisosteres are molecules with different substituents but similar shapes. They are widely used in drug design to modify metabolism, bioavailability, and activity. However, predicting the affinity of bioisosteres with computational methods has been challenging due to their similarity to standard force fields. In this study, a quantum mechanical (QM)-cluster approach based on the GFN2-xTB method was developed and successfully applied to predict the biological activity change of H -> F bioisosteric replacements. The method showed superior accuracy compared to the ChemPLP scoring function and comparable to in vitro experiments, with a standard deviation of 0.60 kcal/mol.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Medicinal
Natalie Losada, Francesc X. Ruiz, Francesca Curreli, Kevin Gruber, Alyssa Pilch, Kalyan Das, Asim K. Debnath, Eddy Arnold
Summary: This study focuses on compounds (NBD derivatives) originally developed to bind to HIV-1 gp120, some of which inhibit RT. Crystal structures of three NBD compounds in complex with HIV-1 RT have been determined, correlating with RT enzyme inhibition and antiviral activity, to develop structure-activity relationships. Two lead compounds, NBD-14189 and NBD-14270, show potent antiviral activity and low cytotoxicity.
JOURNAL OF MEDICINAL CHEMISTRY
(2021)