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)
Article
Chemistry, Multidisciplinary
Guangyan Zhou, Li He, Kathy H. Li, Cassio C. S. Pedroso, Miriam Gochin
Summary: The study presented a low molecular weight covalent inhibitor targeting a conserved lysine residue within the hydrophobic pocket of HIV-1 glycoprotein-41, which exhibited significantly enhanced anti-viral activity compared to its non-covalent counterpart. This represents a major advancement in the quest for non-peptide fusion inhibitors.
CHEMICAL COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Tomonori Shibata, Yasumasa Matsumoto, Akiko Iihara, Kazunori Yamada, Hiroshi Ochiai, Ryo Saito, Shinichi Kusaka, Toshiyuki Kume
Summary: We have developed a selective fluorescent indicator called NBD-NCD that can quench fluorescence when binding to RNA, but can recover fluorescence when displaced by UGGAA repeat-targeted small molecules. The fluorescent indicator displacement assay involving NBD-NCD can be used to detect the interaction between small molecules and UGGAA repeats.
CHEMICAL COMMUNICATIONS
(2023)
Editorial Material
Biochemistry & Molecular Biology
Daniel J. Salamango, Reuben S. Harris
Summary: HIV-1 Vif, in addition to its canonical function of degrading APOBEC3, can also induce potent cell cycle arrest through a newly defined mechanism. Recent advances suggest that the scope of this activity may extend beyond subverting the host cell cycle.
TRENDS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Jack A. Collora, Ya-Chi Ho
Summary: HIV-1 integration introduces ectopic transcription factor binding sites into host chromatin, serving as an ectopic enhancer that recruits transcription factors, increases chromatin accessibility, changes 3D chromatin interactions, and enhances gene expression.
Article
Chemistry, Medicinal
Ying Yang, Lei Zhang, Jinying Tian, Fei Ye, Zhiyan Xiao
Summary: A hierarchical virtual screening identified four potential PTP1B inhibitors with distinct structures, among which H3 and H9 showed selectivity to PTP1B. Key residues responsible for potent allosteric inhibition and excellent PTP selectivity were identified through molecular dynamics simulations and MM-GBSA calculations, aiding future molecular design of PTP1B allosteric inhibitors.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Multidisciplinary Sciences
Kun-Wei Chan, Christina C. Luo, Hong Lu, Xueling Wu, Xiang-Peng Kong
Summary: Identification of vulnerable sites on HIV-1 envelope defined by broadly neutralizing antibodies (bNAbs) is crucial for vaccine design. The structure of bNAb M4008_N1 in complex with BG505 DS-SOSIP reveals a large, shallow protein epitope surface centered at the V3 crown of gp120. M4008_N1 interacts with gp120 primarily through its hammerhead CDR H3 to form a beta-sheet interaction with the V3 crown hairpin in the prefusion Env trimer conformation.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Nneka Ugwu-Korie, Osbourne Quaye, Edward Wright, Sylvester Languon, Odame Agyapong, Emmanuel Broni, Yash Gupta, Prakasha Kempaiah, Samuel K. Kwofie
Summary: This study identified four potential compounds that mimic VRC01 and inhibit the entry of HIV into target cells by interacting with the CD4-binding site of HIV gp120. These compounds have the potential to be a new class of HIV entry inhibitors.
Article
Microbiology
Gilberto Betancor, Jose M. Jimenez-Guardeno, Steven Lynham, Robin Antrobus, Hataf Khan, Andrew Sobala, Matthew D. J. Dicks, Michael H. Malim
Summary: Dual functions of MX2 in innate immunity against HIV-1 and nuclear import of cellular proteins are regulated by phosphorylation. Interferon-stimulated genes establish an antiviral state by activating expression of antiviral cytokines. MX2 inhibits the nuclear import of HIV-1 through interactions with viral capsid and cellular transport machinery, with phosphorylation of its N-terminal domain regulating its antiviral activity and interactions. Interferon treatment reduces phosphorylation levels, highlighting a homeostatic regulatory mechanism balancing MX2's effects on normal cell function with immunity against HIV-1.
NATURE MICROBIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Jack D. Fradgley, Matthieu Starck, Michel Laget, Emmanuel Bourrier, Elodie Dupuis, Laurent Lamarque, Eric Trinquet, Jurriaan M. Zwier, David Parker
Summary: The study introduces pH responsive luminescent europium (III) probes that can be conjugated to targeting vectors to monitor receptor internalization in cells, improving the performance of time-resolved internalization assays that require real-time pH monitoring.
CHEMICAL COMMUNICATIONS
(2021)
Article
Biophysics
Arpa Hudait, James H. Hurley, Gregory A. Voth
Summary: In the late stages of the HIV-1 life cycle, the membrane localization and self-assembly of Gag polyproteins induce membrane deformation and budding. The release of the virion requires the interaction between Gag lattice and ESCRT machinery at the viral budding site, followed by the assembly of downstream ESCRT-III factors. However, the molecular details of upstream ESCRT assembly dynamics remain unclear. In this study, molecular simulations were used to investigate the interactions between Gag, ESCRT-I, ESCRT-II, and membrane, revealing the mechanisms by which upstream ESCRTs assemble at the viral budding site.
BIOPHYSICAL JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Takuya Kobayakawa, Masaru Yokoyama, Kohei Tsuji, Masayuki Fujino, Masaki Kurakami, Sayaka Boku, Miyuki Nakayama, Moemi Kaneko, Nami Ohashi, Osamu Kotani, Tsutomu Murakami, Hironori Sato, Hirokazu Tamamura
Summary: A small molecule designed to mimic hydrophobic interactions between HIV-1 capsid proteins has shown significant anti-HIV-1 activity. Structure activity relationship (SAR) studies of its derivatives provide valuable information for the design and development of novel anti-HIV agents targeting the capsid protein. This new drug has the potential to be an effective treatment for HIV in the future.
Article
Multidisciplinary Sciences
Nicolas Vabret, Valerie Najburg, Alexander Solovyov, Ramya Gopal, Christopher McClain, Petr Sulc, Sreekumar Balan, Yannis Rahou, Guillaume Beauclair, Maxime Chazal, Hugo Varet, Rachel Legendre, Odile Sismeiro, Raul Y. Sanchez David, Lise Chauveau, Nolwenn Jouvenet, Martin Markowitz, Sylvie van der Werf, Olivier Schwartz, Frederic Tangy, Nina Bhardwaj, Benjamin D. Greenbaum, Anastassia V. Komarova
Summary: This study reveals the role of endogenous RNA in antiviral immunity, particularly in interaction with RLRs during different types of RNA virus infections. Specific endogenous RNAs bind to RLRs and induce immune response, indicating the importance of endogenous ligands in PRR activation.
Article
Biology
Akinobu Senoo, Sho Ito, Satoru Nagatoishi, Yutaro Saito, Go Ueno, Daisuke Kuroda, Kouhei Yoshida, Takumi Tashima, Shota Kudo, Shinsuke Sando, Kouhei Tsumoto
Summary: The study identified a chemical fragment specific to P-cadherin that inhibits P-cadherin-mediated cell adhesion. Despite being a fragment compound, it indirectly prevents the formation of hydrogen bonds necessary for X dimer formation by binding to a cavity of P-cadherin, thereby modulating the process of X dimerization.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Wipawee Nittayananta, Aornrutai Promsong, Claire Levy, Florian Hladik, Nithinart Chaitaveep, Suwipa Ungphaiboon, Supinya Tewtrakul, Surada Satthakarn
Summary: This study investigated the effects of ellagic acid (EA) on HIV-1 replication, viral enzyme activity, and cytokine secretion in vitro. The results showed that EA inhibited the replication of R5-tropic HIV-1 and had a dose-dependent inhibitory effect on the virus. Additionally, EA formulated as a gel demonstrated even stronger antiviral effects. The study concluded that EA, whether in solution or gel form, could inhibit HIV infection without adverse effects on target cells.
Letter
Hematology
Adelina Sergueeva, Galina Miasnikova, Binal N. Shah, Jihyun Song, Ekaterina Lisina, Daniel J. Okhotin, Mehdi Nouraie, Sergei Nekhai, Tatiana Ammosova, Xiao Mei Niu, Josef T. Prchal, Xu Zhang, Victor R. Gordeuk
Article
Immunology
Tatiana Ammosova, Colette A. Pietzsch, Yasemin Saygideger, Andrey Ilatovsky, Xionghao Lin, Andrey Ivanov, Namita Kumari, Marina Jerebtsova, Amol Kulkarni, Michael Petukhov, Aykut Uren, Alexander Bukreyev, Sergei Nekhai
JOURNAL OF INFECTIOUS DISEASES
(2018)
Article
Virology
Brian D. Carey, Tatiana Ammosova, Chelsea Pinkham, Xionghao Lin, Weidong Zhou, Lance A. Liotta, Sergei Nekhai, Kylene Kehn-Hall
JOURNAL OF VIROLOGY
(2018)
Article
Biochemistry & Molecular Biology
Andrey Ivanov, Palaniappan Ramanathan, Christian Parry, Philipp A. Ilinykh, Xionghao Lin, Michael Petukhov, Yuri Obukhov, Tatiana Ammosova, Gaya K. Amarasinghe, Alexander Bukreyev, Sergei Nekhai
CELLULAR AND MOLECULAR LIFE SCIENCES
(2020)
Article
Microbiology
Xionghao Lin, Tatiana Ammosova, Meng S. Choy, Colette A. Pietzsch, Andrey Ivanov, Asrar Ahmad, Yasemin Saygideger, Namita Kumari, Dmytro Kovalskyy, Aykut Uren, Wolfgang Peti, Alexander Bukreyev, Sergei Nekhai
FRONTIERS IN MICROBIOLOGY
(2019)
Article
Microbiology
Patrick Younan, Rodrigo I. Santos, Palaniappan Ramanathan, Mathieu Iampietro, Andrew Nishida, Mukta Dutta, Tatiana Ammosova, Michelle Meyer, Michael G. Katze, Vsevolod L. Popov, Sergei Nekhai, Alexander Bukreyev
Article
Biochemistry & Molecular Biology
Alexey Rayevsky, Maxim Platonov, Vasyl Hurmach, Anastasia Yakovenko, Dmitriy Volochnyuk
JOURNAL OF CELLULAR BIOCHEMISTRY
(2020)
Article
Chemistry, Physical
Andrii Malashchuk, Anton Chernykh, Vasyl V. Hurmach, Maxim O. Platonov, Oleksandra Onopchenko, Sergey Zozulya, Constantin G. Daniliuc, Alexey Dobrydnev, Ivan S. Kondratov, Yuriy S. Moroz, Oleksandr O. Grygorenko
JOURNAL OF MOLECULAR STRUCTURE
(2020)
Article
Chemistry, Inorganic & Nuclear
Svitlana Orysyk, Sviatoslav Baranets, Polina Borovyk, Larysa G. Palchykovska, Yurii L. Zborovskii, Viktor V. Orysyk, Artur F. Likhanov, Maxim O. Platonov, Dmytro B. Kovalskyy, Tatyana Shyryna, Yelyzaveta Danylenko, Vasyl V. Hurmach, Vasyl Pekhnyo, Mykhailo V. Vovk
Summary: Five pi-complexes were obtained by reactions between [MCl4](2-) and 1-allyl-3-(2-hydroxyethyl)thiourea (HL) in the presence of HCl and/or KBr/KI, with Cl- and Br-containing chelated pi-type complexes reported for the first time. The structures of these complexes are similar to cisplatin, and different halide anions influence their cytotoxic activity. Among the new analogues, two promising platinum pi-complexes were found to impact cell division and nucleus size, while molecular docking studies indicated DNA plasmid breaks as a mechanism of action.
Article
Hematology
Namita Kumari, Mehdi Nouraie, Asrar Ahmad, Hatajai Lassiter, Javed Khan, Sharmin Diaz, Nowah Afangbedji, Songping Wang, Patricia E. Houston, Tatiana Ammosova, Miguel de Mulder Rougvie, Sohail Rana, Douglas F. Nixon, Kathryn Anastos, Jason Lazar, Audrey L. French, Stephen Gange, Adaora A. Adimora, M. Neale Weitzmann, Margaret Fischl, Mirjam-Colette Kempf, Seble Kassaye, James G. Taylor, Sergei Nekhai
Summary: Individuals with sickle cell trait (SCT) exhibit a restriction of HIV-1 infection characterized by higher levels of HO-1 and lower levels of HIV-1 replication. This suggests that factors like HO-1 and RNR2 may limit HIV-1 pathogenicity among those with SCT.
Article
Chemistry, Multidisciplinary
Lina T. Al Kury, Dimitrios Papandreou, Vasyl V. Hurmach, Dariia O. Dryn, Mariia I. Melnyk, Maxim O. Platonov, Yuriy I. Prylutskyy, Uwe Ritter, Peter Scharff, Alexander V. Zholos
Summary: This study demonstrates that carboxylated single-walled carbon nanotubes can inhibit muscarinic receptor cation current in mouse ileal smooth muscle cells, mainly through direct blocking of the TRPC4 channel.
Article
Biochemistry & Molecular Biology
Andrii A. Zaremba, Polina Y. Zaremba, Maxim O. Platonov
Summary: Epstein-Barr virus is a DNA-containing virus associated with approximately 1% of all cancers. This study focuses on a low molecular weight inhibitor called EBAI, which shows high affinity for the BHRF1 protein of the virus. In vitro studies are needed to fully evaluate EBAI's potential as an inhibitor of the virus's antiapoptotic protein.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemical Research Methods
Xionghao Lin, Asrar Ahmad, Andrey I. Ivanov, Jyothirmai Simhadri, Songping Wang, Namita Kumari, Tatiana Ammosova, Sergei Nekhai
Summary: The HIV-1 transcription inhibitor 1E7-03 reprogrammed the PPAR alpha/RXR alpha and TGF-6 pathways, leading to the inhibition of HIV-1 transcription. The reduced phosphorylation of nucleophosmin and transforming growth factor-beta 2 played important roles in this process. Additionally, phosphorylation of NPM1 was identified as a crucial mechanism for HIV-1 transcription.
MOLECULAR & CELLULAR PROTEOMICS
(2023)
Article
Chemistry, Organic
Alexander Strizhak, Oleg Babii, Sergii Afonin, Iuliia Bakanovich, Teodors Pantelejevs, Wenshu Xu, Elaine Fowler, Rohan Eapen, Krishna Sharma, Maxim O. Platonov, Vasyl V. Hurmach, Laura Itzhaki, Marko Hyvonen, Anne S. Ulrich, David R. Spring, Igor Komarov
ORGANIC & BIOMOLECULAR CHEMISTRY
(2020)
Proceedings Paper
Computer Science, Information Systems
Harry Shaw, Nagarajan Pattabiraman, Deborah Preston, Tatiana Ammosova, Yuri Obukhov, Sergei Nekhai, Ajit Kumar
2019 53RD ANNUAL CONFERENCE ON INFORMATION SCIENCES AND SYSTEMS (CISS)
(2019)