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Shiryaev SA, Cieplak P, Cheltsov A, Liddington RC, Terskikh AV. Dual function of Zika virus NS2B-NS3 protease. PLoS Pathog 2023; 19:e1011795. [PMID: 38011215 PMCID: PMC10723727 DOI: 10.1371/journal.ppat.1011795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/15/2023] [Accepted: 11/02/2023] [Indexed: 11/29/2023] Open
Abstract
Zika virus (ZIKV) serine protease, indispensable for viral polyprotein processing and replication, is composed of the membrane-anchored NS2B polypeptide and the N-terminal domain of the NS3 polypeptide (NS3pro). The C-terminal domain of the NS3 polypeptide (NS3hel) is necessary for helicase activity and contains an ATP-binding site. We discovered that ZIKV NS2B-NS3pro binds single-stranded RNA with a Kd of ~0.3 μM, suggesting a novel function. We tested various structural modifications of NS2B-NS3pro and observed that constructs stabilized in the recently discovered "super-open" conformation do not bind RNA. Likewise, stabilizing NS2B-NS3pro in the "closed" (proteolytically active) conformation using substrate inhibitors abolished RNA binding. We posit that RNA binding occurs when ZIKV NS2B-NS3pro adopts the "open" conformation, which we modeled using highly homologous dengue NS2B-NS3pro crystallized in the open conformation. We identified two positively charged fork-like structures present only in the open conformation of NS3pro. These forks are conserved across Flaviviridae family and could be aligned with the positively charged grove on NS3hel, providing a contiguous binding surface for the negative RNA strand exiting helicase. We propose a "reverse inchworm" model for a tightly intertwined NS2B-NS3 helicase-protease machinery, which suggests that NS2B-NS3pro cycles between open and super-open conformations to bind and release RNA enabling long-range NS3hel processivity. The transition to the closed conformation, likely induced by the substrate, enables the classical protease activity of NS2B-NS3pro.
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Affiliation(s)
- Sergey A. Shiryaev
- Sanford-Burnham-Prebys Medical Discovery Institute, Infectious and Inflammatory Disease Center, La Jolla, California, United States of America
| | - Piotr Cieplak
- Sanford-Burnham-Prebys Medical Discovery Institute, Infectious and Inflammatory Disease Center, La Jolla, California, United States of America
| | - Anton Cheltsov
- Q-mol LLC, San Diego, California, United States of America
| | - Robert C. Liddington
- Sanford-Burnham-Prebys Medical Discovery Institute, Infectious and Inflammatory Disease Center, La Jolla, California, United States of America
| | - Alexey V. Terskikh
- Sanford-Burnham-Prebys Medical Discovery Institute, Infectious and Inflammatory Disease Center, La Jolla, California, United States of America
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Cheltsov A, Nomura N, Yenugonda VM, Roper J, Mukthavaram R, Jiang P, Her NG, Babic I, Kesari S, Nurmemmedov E. Allosteric inhibitor of β-catenin selectively targets oncogenic Wnt signaling in colon cancer. Sci Rep 2020; 10:8096. [PMID: 32415084 PMCID: PMC7229215 DOI: 10.1038/s41598-020-60784-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 02/13/2020] [Indexed: 12/31/2022] Open
Abstract
Abnormal regulation of β-catenin initiates an oncogenic program that serves as a main driver of many cancers. Albeit challenging, β-catenin is an attractive drug target due to its role in maintenance of cancer stem cells and potential to eliminate cancer relapse. We have identified C2, a novel β-catenin inhibitor, which is a small molecule that binds to a novel allosteric site on the surface of β-catenin. C2 selectively inhibits β-catenin, lowers its cellular load and significantly reduces viability of β-catenin-driven cancer cells. Through direct binding to β-catenin, C2 renders the target inactive that eventually activates proteasome system for its removal. Here we report a novel pharmacologic approach for selective inhibition of β-catenin via targeting a cryptic allosteric modulation site. Our findings may provide a new perspective for therapeutic targeting of β-catenin.
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Affiliation(s)
- Anton Cheltsov
- Q-MOL LLC, San Diego, California, United States of America
| | - Natsuko Nomura
- John Wayne Cancer Institute and Pacific Neuroscience Institute at Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Venkata M Yenugonda
- John Wayne Cancer Institute and Pacific Neuroscience Institute at Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Jatin Roper
- Division of Gastroenterology, Department of Medicine, Duke University, Durham, North Carolina, 27710, USA
| | - Rajesh Mukthavaram
- Translational Neuro-Oncology Laboratories, Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - Pengfei Jiang
- Translational Neuro-Oncology Laboratories, Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - Nam-Gu Her
- Korea Institute of Radiological and Medical Sciences, 75 Nowon-ro, Seoul, 01812, Korea
| | - Ivan Babic
- John Wayne Cancer Institute and Pacific Neuroscience Institute at Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Santosh Kesari
- John Wayne Cancer Institute and Pacific Neuroscience Institute at Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Elmar Nurmemmedov
- John Wayne Cancer Institute and Pacific Neuroscience Institute at Providence Saint John's Health Center, Santa Monica, CA, USA.
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Nazario de Moraes L, Tommasini Grotto RM, Targino Valente G, de Carvalho Sampaio H, Magro AJ, Fogaça L, Wolf IR, Perahia D, Faria Silva G, Plana Simões R. A novel molecular mechanism to explain mutations of the HCV protease associated with resistance against covalently bound inhibitors. Virus Res 2019; 274:197778. [PMID: 31618615 DOI: 10.1016/j.virusres.2019.197778] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 10/07/2019] [Accepted: 10/08/2019] [Indexed: 02/07/2023]
Abstract
NS3 is an important therapeutic target for direct-acting antiviral (DAA) drugs. However, many patients treated with DAAs have unsustained virologic response (UVR) due to the high mutation rate of HCV. The aim of this work was to shed some light on the puzzling molecular mechanisms of the virus's of patients who showed high viral loads even under treatment with DAA. Bioinformatics tools, molecular modelling analyses were employed to identify mutations associated with HCV resistance to boceprevir and possible structural features related to this phenomenon. We identified two mutations of NS3 that may be associated with HCV resistance: D168N and L153I. The substitution D168N was previously reported in the literature as related with drug failure. Additionally, we identified that its molecular resistance mechanism can be explained by the destabilization of receptor-ligand hydrogen bonds. For the L153I mutation, the resistance mechanism is different from previous models reported in the literature. The L153I substitution decreases the S139 deprotonation susceptibility, and consequently, this mutation impairs the covalent binding between the residue S139 from NS3 and the electrophilic trap on boceprevir, which can induce drug failure. These results were supported by the time course analysis of the mutations of the NS3 protease, which showed that boceprevir was designed for enzymes with an L residue at position 153; however, the sequences with I153 are predominant nowadays. The results presented here could be used to infer about resistance in others DAA, mainly protease inhibitors.
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Affiliation(s)
- Leonardo Nazario de Moraes
- Sao Paulo State University (UNESP), School of Agriculture, Department of Bioprocess and Biotechnology, Avenue Universitária, 3780, Botucatu, SP, Brazil
| | - Rejane Maria Tommasini Grotto
- Sao Paulo State University (UNESP), School of Agriculture, Department of Bioprocess and Biotechnology, Avenue Universitária, 3780, Botucatu, SP, Brazil; Sao Paulo State University (UNESP), Medical School, Blood Center, Avenue Prof. Mário Rubens Guimarães Montenegro, s/n, Botucatu, SP, Brazil
| | - Guilherme Targino Valente
- Sao Paulo State University (UNESP), School of Agriculture, Department of Bioprocess and Biotechnology, Avenue Universitária, 3780, Botucatu, SP, Brazil; Max Planck Institut for Heart and Lung Research, Ludwigstraße 43, 61231, Bad Nauheim, Germany
| | - Heloisa de Carvalho Sampaio
- Sao Paulo State University (UNESP), Medical School, Blood Center, Avenue Prof. Mário Rubens Guimarães Montenegro, s/n, Botucatu, SP, Brazil
| | - Angelo José Magro
- Sao Paulo State University (UNESP), School of Agriculture, Department of Bioprocess and Biotechnology, Avenue Universitária, 3780, Botucatu, SP, Brazil; Sao Paulo State University (UNESP), Medical School, Blood Center, Avenue Prof. Mário Rubens Guimarães Montenegro, s/n, Botucatu, SP, Brazil; Sao Paulo State University (UNESP), Institute of Biosciences, Street Prof. Dr. Antônio Celso Wagner Zanin, 250, Botucatu, SP, Brazil
| | - Lauana Fogaça
- Sao Paulo State University (UNESP), School of Agriculture, Department of Bioprocess and Biotechnology, Avenue Universitária, 3780, Botucatu, SP, Brazil; Sao Paulo State University (UNESP), Institute of Biosciences, Street Prof. Dr. Antônio Celso Wagner Zanin, 250, Botucatu, SP, Brazil
| | - Ivan Rodrigo Wolf
- Sao Paulo State University (UNESP), Institute of Biosciences, Street Prof. Dr. Antônio Celso Wagner Zanin, 250, Botucatu, SP, Brazil
| | - David Perahia
- École Normale Supérieure Paris-Saclay, Laboratory of Biology and Applied Pharmacology, Cachan, 94235, France
| | - Giovanni Faria Silva
- Sao Paulo State University (UNESP), Medical School, Blood Center, Avenue Prof. Mário Rubens Guimarães Montenegro, s/n, Botucatu, SP, Brazil
| | - Rafael Plana Simões
- Sao Paulo State University (UNESP), School of Agriculture, Department of Bioprocess and Biotechnology, Avenue Universitária, 3780, Botucatu, SP, Brazil; Sao Paulo State University (UNESP), Medical School, Blood Center, Avenue Prof. Mário Rubens Guimarães Montenegro, s/n, Botucatu, SP, Brazil.
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Chen F, Chen J, Lin J, Cheltsov AV, Xu L, Chen Y, Zeng Z, Chen L, Huang M, Hu M, Ye X, Zhou Y, Wang G, Su Y, Zhang L, Zhou F, Zhang XK, Zhou H. NSC-640358 acts as RXRα ligand to promote TNFα-mediated apoptosis of cancer cell. Protein Cell 2015; 6:654-666. [PMID: 26156677 PMCID: PMC4537469 DOI: 10.1007/s13238-015-0178-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Accepted: 05/03/2015] [Indexed: 12/18/2022] Open
Abstract
Retinoid X receptor α (RXRα) and its N-terminally truncated version tRXRα play important roles in tumorigenesis, while some RXRα ligands possess potent anti-cancer activities by targeting and modulating the tumorigenic effects of RXRα and tRXRα. Here we describe NSC-640358 (N-6), a thiazolyl-pyrazole derived compound, acts as a selective RXRα ligand to promote TNFα-mediated apoptosis of cancer cell. N-6 binds to RXRα and inhibits the transactivation of RXRα homodimer and RXRα/TR3 heterodimer. Using mutational analysis and computational study, we determine that Arg316 in RXRα, essential for 9-cis-retinoic acid binding and activating RXRα transactivation, is not required for antagonist effects of N-6, whereas Trp305 and Phe313 are crucial for N-6 binding to RXRα by forming extra π–π stacking interactions with N-6, indicating a distinct RXRα binding mode of N-6. N-6 inhibits TR3-stimulated transactivation of Gal4-DBD-RXRα-LBD by binding to the ligand binding pocket of RXRα-LBD, suggesting a strategy to regulate TR3 activity indirectly by using small molecules to target its interacting partner RXRα. For its physiological activities, we show that N-6 strongly inhibits tumor necrosis factor α (TNFα)-induced AKT activation and stimulates TNFα-mediated apoptosis in cancer cells in an RXRα/tRXRα dependent manner. The inhibition of TNFα-induced tRXRα/p85α complex formation by N-6 implies that N-6 targets tRXRα to inhibit TNFα-induced AKT activation and to induce cancer cell apoptosis. Together, our data illustrate a new RXRα ligand with a unique RXRα binding mode and the abilities to regulate TR3 activity indirectly and to induce TNFα-mediated cancer cell apoptosis by targeting RXRα/tRXRα.
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Affiliation(s)
- Fan Chen
- />School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361102 China
- />School of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou, 363000 China
| | - Jiebo Chen
- />School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361102 China
| | - Jiacheng Lin
- />School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361102 China
| | | | - Lin Xu
- />School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361102 China
| | - Ya Chen
- />Cancer Center, Sanford-Burnham Medical Research Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037 USA
| | - Zhiping Zeng
- />School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361102 China
| | - Liqun Chen
- />School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361102 China
| | - Mingfeng Huang
- />School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361102 China
| | - Mengjie Hu
- />School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361102 China
| | - Xiaohong Ye
- />School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361102 China
| | - Yuqi Zhou
- />School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361102 China
| | - Guanghui Wang
- />School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361102 China
| | - Ying Su
- />School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361102 China
- />Cancer Center, Sanford-Burnham Medical Research Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037 USA
| | - Long Zhang
- />Life Science Institute, Zhejiang University, Hangzhou, 310058 China
| | - Fangfang Zhou
- />Institutes of Biology and Medical Sciences, Soochow University, Suzhou, 215123 China
| | - Xiao-kun Zhang
- />School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361102 China
- />Cancer Center, Sanford-Burnham Medical Research Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037 USA
| | - Hu Zhou
- />School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361102 China
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