1
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Li X, Song Y. Targeting SARS-CoV-2 nonstructural protein 3: Function, structure, inhibition, and perspective in drug discovery. Drug Discov Today 2024; 29:103832. [PMID: 37977285 PMCID: PMC10872262 DOI: 10.1016/j.drudis.2023.103832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/06/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
As a highly contagious human pathogen, severe acute respiratory syndrome-associated coronavirus-2 (SARS-CoV-2) has infected billions of people worldwide with more than 6 million deaths. With several effective vaccines and antiviral drugs now available, the SARS-CoV-2 pandemic been brought under control. However, a new pathogenic coronavirus could emerge in the future, given the zoonotic nature of this virus. Natural evolution and drug-induced mutations of SARS-CoV-2 also require continued efforts for new anti-coronavirus drugs. Nonstructural protein (nsp) 3 of CoVs is a large, multifunctional protein, containing a papain-like protease (PLpro) and a macrodomain (Mac1), which are essential for viral replication. Here, we provide a comprehensive review of the function, structure, and inhibition of SARS-CoV/-CoV-2 PLpro and Mac1. We also discuss advances in, and challenges to, the discovery of drugs against these targets.
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Affiliation(s)
- Xin Li
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA.
| | - Yongcheng Song
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA.
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2
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Valipour M, Di Giacomo S, Di Sotto A, Irannejad H. Discovery of Chalcone-Based Hybrid Structures as High Affinity and Site-Specific Inhibitors against SARS-CoV-2: A Comprehensive Structural Analysis Based on Various Host-Based and Viral Targets. Int J Mol Sci 2023; 24:ijms24108789. [PMID: 37240149 DOI: 10.3390/ijms24108789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 05/01/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
Previous studies indicated that natural-based chalcones have significant inhibitory effects on the coronavirus enzymes 3CLpro and PLpro as well as modulation of some host-based antiviral targets (HBATs). In this study, a comprehensive computational and structural study was performed to investigate the affinity of our compound library consisting of 757 chalcone-based structures (CHA-1 to CHA-757) for inhibiting the 3CLpro and PLpro enzymes and against twelve selected host-based targets. Our results indicated that CHA-12 (VUF 4819) is the most potent and multi-target inhibitor in our chemical library over all viral and host-based targets. Correspondingly, CHA-384 and its congeners containing ureide moieties were found to be potent and selective 3CLpro inhibitors, and benzotriazole moiety in CHA-37 was found to be a main fragment for inhibiting the 3CLpro and PLpro. Surprisingly, our results indicate that the ureide and sulfonamide moieties are integral fragments for the optimum 3CLpro inhibition while occupying the S1 and S3 subsites, which is fully consistent with recent reports on the site-specific 3CLpro inhibitors. Finding the multi-target inhibitor CHA-12, previously reported as an LTD4 antagonist for the treatment of inflammatory pulmonary diseases, prompted us to suggest it as a concomitant agent for relieving respiratory symptoms and suppressing COVID-19 infection.
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Affiliation(s)
- Mehdi Valipour
- Razi Drug Research Center, Iran University of Medical Sciences, Tehran 1545913487, Iran
| | - Silvia Di Giacomo
- Department of Physiology and Pharmacology "V. Erspamer", Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Antonella Di Sotto
- Department of Physiology and Pharmacology "V. Erspamer", Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Hamid Irannejad
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari 4847116547, Iran
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3
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Sawang N, Phongphanphanee S, Wong-ekkabut J, Sutthibutpong T. Biophysical Interpretation of Evolutionary Consequences on the SARS-CoV2 Main Protease through Molecular Dynamics Simulations and Network Topology Analysis. J Phys Chem B 2023; 127:2331-2343. [PMID: 36913683 PMCID: PMC10022058 DOI: 10.1021/acs.jpcb.2c08312] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 02/25/2023] [Indexed: 03/14/2023]
Abstract
In this study, we present a combined analysis procedure between atomistic molecular dynamics (MD) simulations and network topology to obtain more understanding on the evolutionary consequences on protein stability and substrate binding of the main protease enzyme of SARS-CoV2. Communicability matrices of the protein residue networks (PRNs) were extracted from MD trajectories of both Mpro enzymes in complex with the nsp8/9 peptide substrate to compare the local communicability within both proteases that would affect the enzyme function, along with biophysical details on global protein conformation, flexibility, and contribution of amino acid side chains to both intramolecular and intermolecular interactions. The analysis displayed the significance of the mutated residue 46 with the highest communicability gain to the binding pocket closure. Interestingly, the mutated residue 134 with the highest communicability loss corresponded to a local structural disruption of the adjacent peptide loop. The enhanced flexibility of the disrupted loop connecting to the catalytic residue Cys145 introduced an extra binding mode that brought the substrate in proximity and could facilitate the reaction. This understanding might provide further help in the drug development strategy against SARS-CoV2 and prove the capability of the combined techniques of MD simulations and network topology analysis as a "reverse" protein engineering tool.
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Affiliation(s)
- Nuttawat Sawang
- Theoretical
and Computational Physics Group, Department of Physics, King Mongkut’s University of Technology Thonburi
(KMUTT), 126 Pracha-Uthit Road, Bang Mod, Thrung Khru, Bangkok 10140, Thailand
- Center
of Excellence in Theoretical and Computational Science (TaCS-CoE),
Faculty of Science, King Mongkut’s
University of Technology Thonburi (KMUTT), 126 Pracha Uthit Rd., Bang Mod, Thung Khru, Bangkok 10140, Thailand
| | - Saree Phongphanphanee
- Computational
Biomodelling Laboratory for Agricultural Science and Technology (CBLAST),
Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Thailand
Center of Excellence in Physics (ThEP Center), Ministry of Higher Education, Science, Research and Innovation, Bangkok 10400, Thailand
- Department
of Materials Science, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Jirasak Wong-ekkabut
- Computational
Biomodelling Laboratory for Agricultural Science and Technology (CBLAST),
Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Thailand
Center of Excellence in Physics (ThEP Center), Ministry of Higher Education, Science, Research and Innovation, Bangkok 10400, Thailand
- Department
of Physics, Faculty of Science, Kasetsart
University, Bangkok 10900, Thailand
| | - Thana Sutthibutpong
- Theoretical
and Computational Physics Group, Department of Physics, King Mongkut’s University of Technology Thonburi
(KMUTT), 126 Pracha-Uthit Road, Bang Mod, Thrung Khru, Bangkok 10140, Thailand
- Center
of Excellence in Theoretical and Computational Science (TaCS-CoE),
Faculty of Science, King Mongkut’s
University of Technology Thonburi (KMUTT), 126 Pracha Uthit Rd., Bang Mod, Thung Khru, Bangkok 10140, Thailand
- Computational
Biomodelling Laboratory for Agricultural Science and Technology (CBLAST),
Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
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4
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Garland O, Ton AT, Moradi S, Smith JR, Kovacic S, Ng K, Pandey M, Ban F, Lee J, Vuckovic M, Worrall LJ, Young RN, Pantophlet R, Strynadka NCJ, Cherkasov A. Large-Scale Virtual Screening for the Discovery of SARS-CoV-2 Papain-like Protease (PLpro) Non-covalent Inhibitors. J Chem Inf Model 2023; 63:2158-2169. [PMID: 36930801 DOI: 10.1021/acs.jcim.2c01641] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
Abstract
The rapid global spread of the SARS-CoV-2 virus facilitated the development of novel direct-acting antiviral agents (DAAs). The papain-like protease (PLpro) has been proposed as one of the major SARS-CoV-2 targets for DAAs due to its dual role in processing viral proteins and facilitating the host's immune suppression. This dual role makes identifying small molecules that can effectively neutralize SARS-CoV-2 PLpro activity a high-priority task. However, PLpro drug discovery faces a significant challenge due to the high mobility and induced-fit effects in the protease's active site. Herein, we virtually screened the ZINC20 database with Deep Docking (DD) to identify prospective noncovalent PLpro binders and combined ultra-large consensus docking with two pharmacophore (ph4)-filtering strategies. The analysis of active compounds revealed their somewhat-limited diversity, likely attributed to the induced-fit nature of PLpro's active site in the crystal structures, and therefore, the use of rigid docking protocols poses inherited limitations. The top hits were assessed against recombinant viral proteins and live viruses, demonstrating desirable inhibitory activities. The best compound VPC-300195 (IC50: 15 μM) ranks among the top noncovalent PLpro inhibitors discovered through in silico methodologies. In the search for novel SARS-CoV-2 PLpro-specific chemotypes, the identified inhibitors could serve as diverse templates for the development of effective noncovalent PLpro inhibitors.
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Affiliation(s)
- Olivia Garland
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada
| | - Anh-Tien Ton
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada
| | - Shoeib Moradi
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Jason R Smith
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada.,Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Suzana Kovacic
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Kurtis Ng
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Mohit Pandey
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada
| | - Fuqiang Ban
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada
| | - Jaeyong Lee
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Marija Vuckovic
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Liam J Worrall
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Robert N Young
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Ralph Pantophlet
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Artem Cherkasov
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada
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5
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Blanchard AE, Gounley J, Bhowmik D, Chandra Shekar M, Lyngaas I, Gao S, Yin J, Tsaris A, Wang F, Glaser J. Language models for the prediction of SARS-CoV-2 inhibitors. THE INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS 2022; 36:587-602. [PMID: 38603308 PMCID: PMC9548488 DOI: 10.1177/10943420221121804] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The COVID-19 pandemic highlights the need for computational tools to automate and accelerate drug design for novel protein targets. We leverage deep learning language models to generate and score drug candidates based on predicted protein binding affinity. We pre-trained a deep learning language model (BERT) on ∼9.6 billion molecules and achieved peak performance of 603 petaflops in mixed precision. Our work reduces pre-training time from days to hours, compared to previous efforts with this architecture, while also increasing the dataset size by nearly an order of magnitude. For scoring, we fine-tuned the language model using an assembled set of thousands of protein targets with binding affinity data and searched for inhibitors of specific protein targets, SARS-CoV-2 Mpro and PLpro. We utilized a genetic algorithm approach for finding optimal candidates using the generation and scoring capabilities of the language model. Our generalizable models accelerate the identification of inhibitors for emerging therapeutic targets.
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Affiliation(s)
| | - John Gounley
- Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | | | | | - Shang Gao
- Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Junqi Yin
- Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | - Feiyi Wang
- Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jens Glaser
- Oak Ridge National Laboratory, Oak Ridge, TN, USA
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6
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Zhao G, Liu X, Wang S, Bai Z, Zhang S, Wang Y, Yu H, Xu X. Hydrogen bonding penalty used for virtual screening to discover potent inhibitors for Papain-Like cysteine proteases of SARS-CoV-2. Chem Biol Drug Des 2022; 100:502-514. [PMID: 35792890 PMCID: PMC9349924 DOI: 10.1111/cbdd.14115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 06/12/2022] [Accepted: 07/03/2022] [Indexed: 11/26/2022]
Abstract
The Papain-Like proteases (PLpro) of SARS-CoV-2 play a crucial role in viral replication and the formation of nonstructural proteins. To find available inhibitors, the 3D structure of PLpro of SARS2 was obtained by homologous modelling, and we used this structure as a target to search for inhibitors through molecular docking and MM/GBSA binding free energy rescoring. A novel hydrogen bonding penalty was applied to the screening process, which meanwhile took desolvation into account. Finally, 61 compounds were acquired and 4 of them with IC50 at micromolar level tested in vitro enzyme activity assay, which includes clinical drugs tegaserod. Considering the importance of crystal water molecules, the 4 compounds were re-docked and considered bound waters in the active site as a part of PLpro. The binding modes of these 4 compounds were further explored with metadynamics simulations. The hits will provide a starting point for future key interactions identified and lead optimization targetting PLpro.
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Affiliation(s)
- Guangjian Zhao
- Key Laboratory of Marine Drugs of Ministry of Education, School of Medicine and PharmacyOcean University of ChinaQingdaoChina
- Pilot National Laboratory for Marine Science and TechnologyCenter for Innovation Marine Drug Screening & EvaluationQingdaoChina
- Marine Biomedical Research Institute of QingdaoQingdaoChina
| | - Xiaochun Liu
- Key Laboratory of Marine Drugs of Ministry of Education, School of Medicine and PharmacyOcean University of ChinaQingdaoChina
- Pilot National Laboratory for Marine Science and TechnologyCenter for Innovation Marine Drug Screening & EvaluationQingdaoChina
- Marine Biomedical Research Institute of QingdaoQingdaoChina
| | - Suyun Wang
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega‐ScienceWuhan Institute of Virology, Chinese Academy of SciencesWuhanChina
| | - Zhongyue Bai
- Key Laboratory of Marine Drugs of Ministry of Education, School of Medicine and PharmacyOcean University of ChinaQingdaoChina
- Pilot National Laboratory for Marine Science and TechnologyCenter for Innovation Marine Drug Screening & EvaluationQingdaoChina
- Marine Biomedical Research Institute of QingdaoQingdaoChina
| | - Siyu Zhang
- Pilot National Laboratory for Marine Science and TechnologyCenter for Innovation Marine Drug Screening & EvaluationQingdaoChina
- Marine Biomedical Research Institute of QingdaoQingdaoChina
- School of Life ScienceLanzhou UniversityLanzhouChina
| | - Yifan Wang
- Pilot National Laboratory for Marine Science and TechnologyCenter for Innovation Marine Drug Screening & EvaluationQingdaoChina
- Marine Biomedical Research Institute of QingdaoQingdaoChina
- College of Food Science and EngineeringOcean University of ChinaQingdaoChina
| | - Haibo Yu
- School of Chemistry and Molecular BioscienceUniversity of WollongongWollongongNew South WalesAustralia
| | - Ximing Xu
- Key Laboratory of Marine Drugs of Ministry of Education, School of Medicine and PharmacyOcean University of ChinaQingdaoChina
- Pilot National Laboratory for Marine Science and TechnologyCenter for Innovation Marine Drug Screening & EvaluationQingdaoChina
- Marine Biomedical Research Institute of QingdaoQingdaoChina
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7
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Zou Z, Shan H, Sun D, Xia L, Shi Y, Wan J, Zhou A, Wu Y, Xu H, Lei H, Xu Z, Wu Y. Parthenolide reveals an allosteric mode to inhibit the deISGylation activity of SARS-CoV‑2 papain-like protease. Acta Biochim Biophys Sin (Shanghai) 2022; 54:1133-1139. [PMID: 35866602 PMCID: PMC9827819 DOI: 10.3724/abbs.2022092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The coronavirus papain-like protease (PLpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for viral polypeptide cleavage and the deISGylation of interferon-stimulated gene 15 (ISG15), which enable it to participate in virus replication and host innate immune pathways. Therefore, PLpro is considered an attractive antiviral drug target. Here, we show that parthenolide, a germacrane sesquiterpene lactone, has SARS-CoV-2 PLpro inhibitory activity. Parthenolide covalently binds to Cys-191 or Cys-194 of the PLpro protein, but not the Cys-111 at the PLpro catalytic site. Mutation of Cys-191 or Cys-194 reduces the activity of PLpro. Molecular docking studies show that parthenolide may also form hydrogen bonds with Lys-192, Thr-193, and Gln-231. Furthermore, parthenolide inhibits the deISGylation but not the deubiquitinating activity of PLpro in vitro. These results reveal that parthenolide inhibits PLpro activity by allosteric regulation.
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Affiliation(s)
- Zhihui Zou
- Hongqiao International Institute of MedicineShanghai Tongren Hospital / Faculty of Basic MedicineChemical Biology Division of Shanghai Universities E-InstitutesKey Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of EducationChinese Academy of Medical Sciences Research Unit 2019RU043Shanghai Jiao Tong University School of Medicine (SJTU-SM)Shanghai200025China
| | - Huizhuang Shan
- Hongqiao International Institute of MedicineShanghai Tongren Hospital / Faculty of Basic MedicineChemical Biology Division of Shanghai Universities E-InstitutesKey Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of EducationChinese Academy of Medical Sciences Research Unit 2019RU043Shanghai Jiao Tong University School of Medicine (SJTU-SM)Shanghai200025China,Laboratory MedicineGuangdong Provincial People’s HospitalGuangdong Academy of Medical SciencesGuangzhouGuangdong510000China
| | - Demeng Sun
- Tsinghua-Peking Center for Life SciencesKey Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education)Beijing Advanced Innovation Center for Structural BiologyDepartment of ChemistryTsinghua UniversityBeijing100084China
| | - Li Xia
- Hongqiao International Institute of MedicineShanghai Tongren Hospital / Faculty of Basic MedicineChemical Biology Division of Shanghai Universities E-InstitutesKey Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of EducationChinese Academy of Medical Sciences Research Unit 2019RU043Shanghai Jiao Tong University School of Medicine (SJTU-SM)Shanghai200025China
| | - Yulong Shi
- CAS Key Laboratory of Receptor ResearchDrug Discovery and Design CenterShanghai Institute of Materia MedicaChinese Academy of SciencesShanghai201203China
| | - Jiahui Wan
- Hongqiao International Institute of MedicineShanghai Tongren Hospital / Faculty of Basic MedicineChemical Biology Division of Shanghai Universities E-InstitutesKey Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of EducationChinese Academy of Medical Sciences Research Unit 2019RU043Shanghai Jiao Tong University School of Medicine (SJTU-SM)Shanghai200025China
| | - Aiwu Zhou
- Hongqiao International Institute of MedicineShanghai Tongren Hospital / Faculty of Basic MedicineChemical Biology Division of Shanghai Universities E-InstitutesKey Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of EducationChinese Academy of Medical Sciences Research Unit 2019RU043Shanghai Jiao Tong University School of Medicine (SJTU-SM)Shanghai200025China
| | - Yunzhao Wu
- Hongqiao International Institute of MedicineShanghai Tongren Hospital / Faculty of Basic MedicineChemical Biology Division of Shanghai Universities E-InstitutesKey Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of EducationChinese Academy of Medical Sciences Research Unit 2019RU043Shanghai Jiao Tong University School of Medicine (SJTU-SM)Shanghai200025China
| | - Hanzhang Xu
- Hongqiao International Institute of MedicineShanghai Tongren Hospital / Faculty of Basic MedicineChemical Biology Division of Shanghai Universities E-InstitutesKey Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of EducationChinese Academy of Medical Sciences Research Unit 2019RU043Shanghai Jiao Tong University School of Medicine (SJTU-SM)Shanghai200025China
| | - Hu Lei
- Hongqiao International Institute of MedicineShanghai Tongren Hospital / Faculty of Basic MedicineChemical Biology Division of Shanghai Universities E-InstitutesKey Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of EducationChinese Academy of Medical Sciences Research Unit 2019RU043Shanghai Jiao Tong University School of Medicine (SJTU-SM)Shanghai200025China
| | - Zhijian Xu
- CAS Key Laboratory of Receptor ResearchDrug Discovery and Design CenterShanghai Institute of Materia MedicaChinese Academy of SciencesShanghai201203China,Correspondence address. +86-21-63846590-776916; E-mail: (Y.W.) / Tel: +86-21-50806600-1304; E-mail: (Z.X.) @simm.ac.cn
| | - Yingli Wu
- Hongqiao International Institute of MedicineShanghai Tongren Hospital / Faculty of Basic MedicineChemical Biology Division of Shanghai Universities E-InstitutesKey Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of EducationChinese Academy of Medical Sciences Research Unit 2019RU043Shanghai Jiao Tong University School of Medicine (SJTU-SM)Shanghai200025China,Correspondence address. +86-21-63846590-776916; E-mail: (Y.W.) / Tel: +86-21-50806600-1304; E-mail: (Z.X.) @simm.ac.cn
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8
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Ferreira GM, Pillaiyar T, Hirata MH, Poso A, Kronenberger T. Inhibitor induced conformational changes in SARS-COV-2 papain-like protease. Sci Rep 2022; 12:11585. [PMID: 35803957 PMCID: PMC9270405 DOI: 10.1038/s41598-022-15181-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 06/20/2022] [Indexed: 01/24/2023] Open
Abstract
SARS-CoV-2's papain-like protease (PLpro) interaction with ligands has recently been explored with a myriad of crystal structures. We used molecular dynamics (MD) simulations to study different PLpro-ligand complexes, their ligand-induced conformational changes, and interactions. We focused on inhibitors reported with known IC50 against PLpro, namely GRL-0617, XR8-89, PLP_Snyder530, and Sander's recently published compound 7 (CPD7), and compared these trajectories against the apostructure (Apo), with a total of around 60 µs worth simulation data. We aimed to study the conformational changes using molecular dynamics simulations for the inhibitors in the PLpro. PCA analyses and the MSM models revealed distinct conformations of PLpro in the absence/presence of ligands and proposed that BL2-loop contributes to the accessibility of these inhibitors. Further, bulkier substituents closer to Tyr268 and Gln269 could improve inhibition of SARS-CoV-2 PLpro by occupying the region between BL2-groove and BL2-loop, but we also expand on the relevance of exploring multiple PLpro sub-pockets to improve inhibition.
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Affiliation(s)
- Glaucio Monteiro Ferreira
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Av Prof Lineu Prestes 580, São Paulo, 05508-000, Brazil
| | - Thanigaimalai Pillaiyar
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Mario Hiroyuki Hirata
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Av Prof Lineu Prestes 580, São Paulo, 05508-000, Brazil
| | - Antti Poso
- Department of Oncology and Pneumonology, Internal Medicine VIII, University Hospital Tübingen, Otfried-Müller-Straße 10, 72076, Tübingen, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Thales Kronenberger
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany.
- Department of Oncology and Pneumonology, Internal Medicine VIII, University Hospital Tübingen, Otfried-Müller-Straße 10, 72076, Tübingen, Germany.
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211, Kuopio, Finland.
- Tübingen Center for Academic Drug Discovery and Development (TüCAD2), 72076, Tübingen, Germany.
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9
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Freitas BT, Ahiadorme DA, Bagul RS, Durie IA, Ghosh S, Hill J, Kramer NE, Murray J, O’Boyle BM, Onobun E, Pirrone MG, Shepard JD, Enos S, Subedi YP, Upadhyaya K, Tripp RA, Cummings BS, Crich D, Pegan SD. Exploring Noncovalent Protease Inhibitors for the Treatment of Severe Acute Respiratory Syndrome and Severe Acute Respiratory Syndrome-Like Coronaviruses. ACS Infect Dis 2022; 8:596-611. [PMID: 35199517 PMCID: PMC8887654 DOI: 10.1021/acsinfecdis.1c00631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Indexed: 12/21/2022]
Abstract
Over the last 20 years, both severe acute respiratory syndrome coronavirus-1 and severe acute respiratory syndrome coronavirus-2 have transmitted from animal hosts to humans causing zoonotic outbreaks of severe disease. Both viruses originate from a group of betacoronaviruses known as subgroup 2b. The emergence of two dangerous human pathogens from this group along with previous studies illustrating the potential of other subgroup 2b members to transmit to humans has underscored the need for antiviral development against them. Coronaviruses modify the host innate immune response in part through the reversal of ubiquitination and ISGylation with their papain-like protease (PLpro). To identify unique or overarching subgroup 2b structural features or enzymatic biases, the PLpro from a subgroup 2b bat coronavirus, BtSCoV-Rf1.2004, was biochemically and structurally evaluated. This evaluation revealed that PLpros from subgroup 2b coronaviruses have narrow substrate specificity for K48 polyubiquitin and ISG15 originating from certain species. The PLpro of BtSCoV-Rf1.2004 was used as a tool alongside PLpro of CoV-1 and CoV-2 to design 30 novel noncovalent drug-like pan subgroup 2b PLpro inhibitors that included determining the effects of using previously unexplored core linkers within these compounds. Two crystal structures of BtSCoV-Rf1.2004 PLpro bound to these inhibitors aided in compound design as well as shared structural features among subgroup 2b proteases. Screening of these three subgroup 2b PLpros against this novel set of inhibitors along with cytotoxicity studies provide new directions for pan-coronavirus subgroup 2b antiviral development of PLpro inhibitors.
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Affiliation(s)
- Brendan T. Freitas
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia 120 W. Green Street, Athens, Georgia 30602, United States
| | - Daniil A. Ahiadorme
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602, United States
| | - Rahul S. Bagul
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia 120 W. Green Street, Athens, Georgia 30602, United States
| | - Ian A. Durie
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia 120 W. Green Street, Athens, Georgia 30602, United States
| | - Samir Ghosh
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia 120 W. Green Street, Athens, Georgia 30602, United States
| | - Jarvis Hill
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602, United States
| | - Naomi E. Kramer
- Interdisciplinary Toxicology Program, University of Georgia, Athens, Georgia 30602, United States
| | - Jackelyn Murray
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia 30602, United States
| | - Brady M. O’Boyle
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia 120 W. Green Street, Athens, Georgia 30602, United States
| | - Emmanuel Onobun
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602, United States
| | - Michael G. Pirrone
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia 120 W. Green Street, Athens, Georgia 30602, United States
| | - Justin D. Shepard
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia 30602, United States
| | - Suzanne Enos
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia 120 W. Green Street, Athens, Georgia 30602, United States
| | - Yagya P. Subedi
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia 120 W. Green Street, Athens, Georgia 30602, United States
| | - Kapil Upadhyaya
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia 120 W. Green Street, Athens, Georgia 30602, United States
| | - Ralph A. Tripp
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia 30602, United States
| | - Brian S. Cummings
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia 120 W. Green Street, Athens, Georgia 30602, United States
- Interdisciplinary Toxicology Program, University of Georgia, Athens, Georgia 30602, United States
| | - David Crich
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia 120 W. Green Street, Athens, Georgia 30602, United States
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602, United States
| | - Scott D. Pegan
- Division of Biomedical Sciences, University of California Riverside, Riverside, California, 92521, United States
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10
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Lv Z, Cano KE, Jia L, Drag M, Huang TT, Olsen SK. Targeting SARS-CoV-2 Proteases for COVID-19 Antiviral Development. Front Chem 2022; 9:819165. [PMID: 35186898 PMCID: PMC8850931 DOI: 10.3389/fchem.2021.819165] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 12/20/2021] [Indexed: 12/18/2022] Open
Abstract
The emergence of severe acute respiratory syndrome (SARS-CoV-2) in 2019 marked the third occurrence of a highly pathogenic coronavirus in the human population since 2003. As the death toll surpasses 5 million globally and economic losses continue, designing drugs that could curtail infection and disease progression is critical. In the US, three highly effective Food and Drug Administration (FDA)-authorized vaccines are currently available, and Remdesivir is approved for the treatment of hospitalized patients. However, moderate vaccination rates and the sustained evolution of new viral variants necessitate the ongoing search for new antivirals. Several viral proteins have been prioritized as SARS-CoV-2 antiviral drug targets, among them the papain-like protease (PLpro) and the main protease (Mpro). Inhibition of these proteases would target viral replication, viral maturation, and suppression of host innate immune responses. Knowledge of inhibitors and assays for viruses were quickly adopted for SARS-CoV-2 protease research. Potential candidates have been identified to show inhibitory effects against PLpro and Mpro, both in biochemical assays and viral replication in cells. These results encourage further optimizations to improve prophylactic and therapeutic efficacy. In this review, we examine the latest developments of potential small-molecule inhibitors and peptide inhibitors for PLpro and Mpro, and how structural biology greatly facilitates this process.
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Affiliation(s)
- Zongyang Lv
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Kristin E. Cano
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Lijia Jia
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Marcin Drag
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Tony T. Huang
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, United States
| | - Shaun K. Olsen
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
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11
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Structure-based inhibitor design and repurposing clinical drugs to target SARS-CoV-2 proteases. Biochem Soc Trans 2022; 50:151-165. [PMID: 35015073 DOI: 10.1042/bst20211180] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 01/01/2023]
Abstract
SARS-CoV-2, the coronavirus responsible for the current COVID-19 pandemic, encodes two proteases, 3CLpro and PLpro, two of the main antiviral research targets. Here we provide an overview of the structures and functions of 3CLpro and PLpro and examine strategies of structure-based drug designing and drug repurposing against these proteases. Rational structure-based drug design enables the generation of potent and target-specific antivirals. Drug repurposing offers an attractive prospect with an accelerated turnaround. Thus far, several protease inhibitors have been identified, and some candidates are undergoing trials that may well prove to be effective antivirals against SARS-CoV-2.
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12
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Li L, Ma L, Hu Y, Li X, Yu M, Shang H, Zou Z. Natural biflavones are potent inhibitors against SARS-CoV-2 papain-like protease. PHYTOCHEMISTRY 2022; 193:112984. [PMID: 34757253 PMCID: PMC8506144 DOI: 10.1016/j.phytochem.2021.112984] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 10/01/2021] [Accepted: 10/09/2021] [Indexed: 06/02/2023]
Abstract
Papain-like protease (PLpro) is a key enzyme encoded by SARS-CoV-2 that is essential for viral replication and immune evasion. Significant suppression of viral spread and promotion of antiviral immunity can be achieved by inhibition of PLpro, revealing an inspiring strategy for COVID-19 treatment. This study aimed to discover PLpro inhibitors by investigating the national compound library of traditional Chinese medicines (NCLTCMs), a phytochemical library comprising over 9000 TCM-derived compounds. Through virtual screening and enzymatic evaluations, nine natural biflavones were confirmed to be effective PLpro inhibitors with IC50 values ranging from 9.5 to 43.2 μM. Pro-ISG15 cleavage assays further demonstrated that several biflavones exhibited potent inhibitory effects against PLpro-mediated deISGylation, a key process involved in viral immune evasion. Herein, we report the discovery, antiviral evaluation, structure-activity relationship elucidation and molecular docking investigation of biflavones as potent inhibitors of SARS-CoV-2 PLpro.
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Affiliation(s)
- Lingyu Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, PR China
| | - Liyan Ma
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, PR China
| | - Yue Hu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, PR China
| | - Xiaoxue Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, PR China; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, PR China
| | - Meng Yu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, PR China
| | - Hai Shang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, PR China.
| | - Zhongmei Zou
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, PR China.
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13
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Sanachai K, Mahalapbutr P, Sanghiran Lee V, Rungrotmongkol T, Hannongbua S. In Silico Elucidation of Potent Inhibitors and Rational Drug Design against SARS-CoV-2 Papain-like Protease. J Phys Chem B 2021; 125:13644-13656. [PMID: 34904832 PMCID: PMC8691209 DOI: 10.1021/acs.jpcb.1c07060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/01/2021] [Indexed: 01/08/2023]
Abstract
Global public health has been a critical problem by the sudden increase of the COVID-19 outbreak. The papain-like protease (PLpro) of SARS-CoV-2 is a key promising target for antiviral drug development since it plays a pivotal role in viral replication and innate immunity. Here, we employed the all-atom molecular dynamics (MD) simulations and binding free energy calculations based on MM-PB(GB)SA and SIE methods to elucidate and compare the binding behaviors of five inhibitors derived from peptidomimetic inhibitors (VIR250 and VIR251) and naphthalene-based inhibitors (GRL-0617, compound 3, and compound Y96) against SARS-CoV-2 PLpro. The obtained results revealed that all inhibitors interacting within the PLpro active site are mostly driven by vdW interactions, and the hydrogen bond formation in residues G163 and G271 with peptidomimetics and the Q269 residue with naphthalene-based inhibitors was essential for stabilizing the protein-ligand complexes. Among the five studied inhibitors, VIR250 exhibited the most binding efficiency with SARS-CoV-2 PLpro, and thus, it was chosen for the rational drug design. Based on the computationally designed ligand-protein complexes, the replacement of aromatic rings including heteroatoms (e.g., thiazolopyridine) at the P2 and P4 sites could help to improve the inhibitor-binding efficiency. Furthermore, the hydrophobic interactions with residues at P1-P3 sites can be increased by enlarging the nonpolar moieties (e.g., ethene) at the N-terminal of VIR250. We expect that the structural data obtained will contribute to the development of new PLpro inhibitors with more inhibitory potency for COVID-19.
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Affiliation(s)
- Kamonpan Sanachai
- Center
of Excellence in Computational Chemistry (CECC), Department of Chemistry,
Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Biocatalyst
and Environmental Biotechnology Research Unit, Department of Biochemistry,
Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Panupong Mahalapbutr
- Department
of Biochemistry, Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Vannajan Sanghiran Lee
- Department
of Chemistry, Faculty of Science, University
of Malaya, Kuala
Lumpur 50603, Malaysia
| | - Thanyada Rungrotmongkol
- Biocatalyst
and Environmental Biotechnology Research Unit, Department of Biochemistry,
Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Program
in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
| | - Supot Hannongbua
- Center
of Excellence in Computational Chemistry (CECC), Department of Chemistry,
Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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14
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Alabbas AB, Alamri MA. Analyzing the Effect of Mutations in SARS-CoV2 Papain-Like Protease from Saudi Isolates on Protein Structure and Drug-Protein Binding: Molecular Modelling and Dynamics Studies. Saudi J Biol Sci 2021; 29:526-533. [PMID: 34548835 PMCID: PMC8447498 DOI: 10.1016/j.sjbs.2021.09.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 08/31/2021] [Accepted: 09/09/2021] [Indexed: 02/09/2023] Open
Abstract
The continuous and rapid development of the severe acute
respiratory syndrome coronavirus-2 (SARS-CoV-2) virus remains a health concern
especially with the emergence of numerous variants and mutations worldwide. As
with other RNA viruses, SARS-CoV-2 has a genetically high mutation rate. These
mutations have an impact on the virus characteristics, including
transmissibility, antigenicity and development of drug and vaccine resistance.
This work was pursued to identify the differences that exist in the papain-like
protease (PLPro) from 58 Saudi isolates in comparison to the
first reported sequence from Wuhan, China and determine their implications on
protein structure and the inhibitor binding. PLpro is a key
protease enzyme for the host cells invasion and viral proteolytic cleavage,
hence, it emerges as a valuable antiviral therapeutic target. Two mutations were
identified including D108G and A249V and shown to increase the molecular
flexibility of PLPro protein and alter the protein stability,
particularly with D108G mutation. The effect of these mutations on the stability
and dynamic behavior of PLPro structures as well as their
effect on the binding of a known inhibitor; GRL0617 were further investigated by
molecular docking and dynamic simulation.
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Affiliation(s)
- Alhumaidi B Alabbas
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Mubarak A Alamri
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
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15
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Stasiulewicz A, Maksymiuk AW, Nguyen ML, Bełza B, Sulkowska JI. SARS-CoV-2 Papain-Like Protease Potential Inhibitors-In Silico Quantitative Assessment. Int J Mol Sci 2021; 22:3957. [PMID: 33921228 PMCID: PMC8069282 DOI: 10.3390/ijms22083957] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/26/2021] [Accepted: 04/02/2021] [Indexed: 12/22/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) encodes the papain-like protease (PLpro). The protein not only plays an essential role in viral replication but also cleaves ubiquitin and ubiquitin-like interferon-stimulated gene 15 protein (ISG15) from host proteins, making it an important target for developing new antiviral drugs. In this study, we searched for novel, noncovalent potential PLpro inhibitors by employing a multistep in silico screening of a 15 million compound library. The selectivity of the best-scored compounds was evaluated by checking their binding affinity to the human ubiquitin carboxy-terminal hydrolase L1 (UCH-L1), which, as a deubiquitylating enzyme, exhibits structural and functional similarities to the PLpro. As a result, we identified 387 potential, selective PLpro inhibitors, from which we retrieved the 20 best compounds according to their IC50 values toward PLpro estimated by a multiple linear regression model. The selected candidates display potential activity against the protein with IC50 values in the nanomolar range from approximately 159 to 505 nM and mostly adopt a similar binding mode to the known, noncovalent SARS-CoV-2 PLpro inhibitors. We further propose the six most promising compounds for future in vitro evaluation. The results for the top potential PLpro inhibitors are deposited in the database prepared to facilitate research on anti-SARS-CoV-2 drugs.
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Affiliation(s)
- Adam Stasiulewicz
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland; (A.S.); (A.W.M.); (M.L.N.); (B.B.)
- Faculty of Pharmacy, Medical University of Warsaw, Banacha 1, 02-097 Warsaw, Poland
| | - Alicja W. Maksymiuk
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland; (A.S.); (A.W.M.); (M.L.N.); (B.B.)
- School of the Biological Sciences, University of Cambridge, 17 Mill Lane, Cambridge CB2 1RX, UK
| | - Mai Lan Nguyen
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland; (A.S.); (A.W.M.); (M.L.N.); (B.B.)
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland
| | - Barbara Bełza
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland; (A.S.); (A.W.M.); (M.L.N.); (B.B.)
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Joanna I. Sulkowska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland; (A.S.); (A.W.M.); (M.L.N.); (B.B.)
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