1
|
Nguyen HT, Van KT, Pham-The H, Le QB, Le-Nhat-Thuy G, Dang Thi TA, Hoang Thi P, Nguyen Thi QG, Tuan AN, Vu Ngoc D, Van Nguyen T. Synthesis, cytotoxicity, apoptosis-inducing activity and molecular docking studies of novel isatin-podophyllotoxin hybrids. RSC Adv 2025; 15:2825-2839. [PMID: 39877702 PMCID: PMC11774189 DOI: 10.1039/d4ra08691k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2024] [Accepted: 01/13/2025] [Indexed: 01/31/2025] Open
Abstract
Podophyllotoxin, along with its numerous derivatives and related compounds, is well known for its broad-spectrum pharmacological activity, especially for anticancer potential. In this study, several isatin-podophyllotoxin hybrid compounds were successfully synthesized with good yields through microwave-prompted three-component reactions of 2-amino-1,4-naphthoquinone, various substituted isatins, and tetronic acid. Their cytotoxicity was assessed against four types of human cancer cell lines, HepG2 (hepatoma carcinoma), MCF7 (breast cancer), A549 (non-small lung cancer), and KB (epidermoid carcinoma), alongside nontumorigenic HEK-293 human embryonic kidney cells. Among 14 compounds screened, 7f possessed the strongest cytotoxicity to KB and A549 cell lines, with IC50 values of 1.99 ± 0.22 and 0.90 ± 0.09 μM, respectively. Further studies revealed that product 7f could arrest the cell cycle of A549 cells at S phase and induce apoptosis of A549 cells. This compound was examined for its binding ability against cyclin-dependent kinases (CDKs) and procaspase/caspase systems. The results indicated that 7f exhibited significant interactions with the residues of the ATP binding sites of CDK2/cyclin A and CDK5/p25 and also activated procaspase 6 through stable zinc chelation. Additionally, physicochemical and pharmacokinetic properties related to drug-likeness, in parallel with toxicity, were computationally assessed to identify the main issues that need to be addressed in structural optimization. Taken together, compound 7f was identified as a potent cytotoxic agent that could be considered for anticancer drug discovery and development.
Collapse
Affiliation(s)
- Ha Thanh Nguyen
- Institute of Chemistry, Vietnam Academy of Science and Technology (VAST) 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
- Graduate University of Science and Technology, VAST 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
| | - Ket Tran Van
- Graduate University of Science and Technology, VAST 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
- Military Technical Academy 236 Hoang Quoc Viet, Bac Tu Liem Hanoi Vietnam
| | - Hai Pham-The
- University of Science and Technology of Hanoi, VAST 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
| | - Quang-Bao Le
- University of Science and Technology of Hanoi, VAST 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
| | - Giang Le-Nhat-Thuy
- Institute of Chemistry, Vietnam Academy of Science and Technology (VAST) 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
- Graduate University of Science and Technology, VAST 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
| | - Tuyet Anh Dang Thi
- Institute of Chemistry, Vietnam Academy of Science and Technology (VAST) 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
- Graduate University of Science and Technology, VAST 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
| | - Phuong Hoang Thi
- Institute of Chemistry, Vietnam Academy of Science and Technology (VAST) 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
- Graduate University of Science and Technology, VAST 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
| | - Quynh Giang Nguyen Thi
- Institute of Chemistry, Vietnam Academy of Science and Technology (VAST) 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
| | - Anh Nguyen Tuan
- Institute of Chemistry, Vietnam Academy of Science and Technology (VAST) 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
- Graduate University of Science and Technology, VAST 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
| | - Doan Vu Ngoc
- Military Technical Academy 236 Hoang Quoc Viet, Bac Tu Liem Hanoi Vietnam
| | - Tuyen Van Nguyen
- Institute of Chemistry, Vietnam Academy of Science and Technology (VAST) 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
- Graduate University of Science and Technology, VAST 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
| |
Collapse
|
2
|
Matias-Barrios VM, Radaeva M, Rosellinny G, Jia Q, Xie N, Villanueva M, Ibrahim H, Smith J, Gleave M, Lallous N, Straus SK, Cherkasov A, Dong X. Developing novel Lin28 inhibitors by computer aided drug design. Cell Death Discov 2025; 11:5. [PMID: 39800739 PMCID: PMC11725581 DOI: 10.1038/s41420-024-02281-z] [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: 07/15/2024] [Revised: 12/09/2024] [Accepted: 12/23/2024] [Indexed: 01/16/2025] Open
Abstract
Lin28 is a key regulator of cancer stem cell gene network that promotes therapy-resistant tumor progression in various tumors. However, no Lin28 inhibitor has been approved to treat cancer patients, urging exploration of novel compounds as candidates to be tested for clinical trials. In this contribution, we applied computer-aided drug design (CADD) in combination with quantitative biochemical and biological assays. These efforts led to the discovery of Ln268 as a drug candidate that can block Lin28 from binding to its RNA substrates and inhibit Lin28 activities. Ln268 suppressed Lin28-mediated cancer cell proliferation and spheroid growth. Results from nuclear magnetic resonance spectroscopy confirmed that Ln268 perturbs the conformation of the zinc knuckle domain of Lin28, validating the rational drug design by CADD. The inhibitory effects of Ln268 are dependent on Lin28 protein expression in cancer cells, highlighting limited off-target effects of Ln268. Moreover, Ln268 synergizes with several chemotherapy drugs to suppress tumor cell growth. In summary, Ln268 is a promising candidate for further development to target Lin28 as a cancer therapy.
Collapse
Affiliation(s)
- Victor M Matias-Barrios
- The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak Street, Vancouver, BC, V6H 3Z6, Canada
| | - Mariia Radaeva
- The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak Street, Vancouver, BC, V6H 3Z6, Canada
| | - Graciella Rosellinny
- The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak Street, Vancouver, BC, V6H 3Z6, Canada
| | - Qiongqiong Jia
- The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak Street, Vancouver, BC, V6H 3Z6, Canada
| | - Ning Xie
- The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak Street, Vancouver, BC, V6H 3Z6, Canada
| | - Monica Villanueva
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada
| | - Hanadi Ibrahim
- The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak Street, Vancouver, BC, V6H 3Z6, Canada
| | - Jason Smith
- The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak Street, Vancouver, BC, V6H 3Z6, Canada
| | - Martin Gleave
- The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak Street, Vancouver, BC, V6H 3Z6, Canada
| | - Nada Lallous
- The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak Street, Vancouver, BC, V6H 3Z6, Canada
| | - Suzana K Straus
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada
| | - Artem Cherkasov
- The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak Street, Vancouver, BC, V6H 3Z6, Canada
| | - Xuesen Dong
- The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak Street, Vancouver, BC, V6H 3Z6, Canada.
| |
Collapse
|
3
|
Durmic Z, Duin EC, Bannink A, Belanche A, Carbone V, Carro MD, Crüsemann M, Fievez V, Garcia F, Hristov A, Joch M, Martinez-Fernandez G, Muetzel S, Ungerfeld EM, Wang M, Yáñez-Ruiz DR. Feed additives for methane mitigation: Recommendations for identification and selection of bioactive compounds to develop antimethanogenic feed additives. J Dairy Sci 2025; 108:302-321. [PMID: 39725500 DOI: 10.3168/jds.2024-25045] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 10/15/2024] [Indexed: 12/28/2024]
Abstract
Despite the increasing interest in developing antimethanogenic additives to reduce enteric methane (CH4) emissions and the extensive research conducted over the last decades, the global livestock industry has a very limited number of antimethanogenic feed additives (AMFA) available that can deliver substantial reduction, and they have generally not reached the market yet. This work provides technical recommendations and guidelines for conducting tests intended to screen the potential to reduce, directly or indirectly, enteric CH4 of compounds before they can be further assessed in in vivo conditions. The steps involved in this work cover the discovery, isolation, and identification of compounds capable of affecting CH4 production by rumen microbes, followed by in vitro laboratory testing of potential candidates. The finding of new bioactive compounds as AMFA can be based on 2 approaches: empirical and mechanistic. The empirical approach involves obtaining and screening compounds present in databases and repositories that potentially possess the desired effect but have not yet been tested, screening natural sources of secondary compounds such as plants, fungi, and algae for their antimethanogenic effects, or examining compounds with antimethanogenic effect on microbes in other research domains outside the rumen. In contrast, the mechanistic approach is the theoretical process of discovery new bioactive compounds based on existing knowledge of a biological target or process. The in vitro methodologies reviewed include examining effects at the subcellular level, in single pure cultures of methanogens and examining in more complex mixed rumen microbial populations. Simple in vitro methodologies (subcellular assessments and batch culture) allow testing a large number of compounds, whereas more complex systems simulating the rumen microbial ecosystem can test a limited number of candidates but provide better insight about the antimethanogenic efficacy. This work collated the main advantages, limitations, and technical recommendations associated with each step and methodology use during the identification and screening of AMFA candidates.
Collapse
Affiliation(s)
- Zoey Durmic
- School of Agriculture and Environment, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Evert C Duin
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849
| | - André Bannink
- Wageningen Livestock Research, Wageningen University & Research, 6700 AH Wageningen, the Netherlands
| | - Alejandro Belanche
- Departamento de Producción Animal y Ciencia de los Alimentos, Universidad de Zaragoza, 50013, Zaragoza, Spain
| | | | - M Dolores Carro
- Departamento de Producción Agraria, Universidad Politécnica de Madrid, ETSIAAB, 28040 Madrid, Spain
| | - Max Crüsemann
- Institute of Pharmaceutical Biology, University of Bonn, 53115 Bonn, Germany
| | - Veerle Fievez
- Department of Animal Sciences and Aquatic Ecology, Ghent University, 9000 Gent, Belgium
| | - Florencia Garcia
- Universidad Nacional de Córdoba, Facultad de Ciencias Agropecuarias, Córdoba, 5000, Argentina.
| | - Alex Hristov
- Department of Animal Science, The Pennsylvania State University, University Park, PA 16802
| | - Miroslav Joch
- Department of Nutrition and Feeding of Farm Animals, Institute of Animal Science, 104 00 Prague, Czech Republic
| | | | - Stefan Muetzel
- AgResearch Ltd. Grasslands, Palmerston North, 4442, New Zealand
| | - Emilio M Ungerfeld
- Instituto de Investigaciones Agropecuarias, Centro Regional de Investigación Carillanca, Vilcún, La Araucanía, Chile, 4880000
| | - Min Wang
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, 410125, Changsha, Hunan, China
| | | |
Collapse
|
4
|
Ranaweera KKTN, Baik M. In silico docking and molecular dynamics for the discovery of inhibitors of enteric methane production in ruminants - A review. Anim Biosci 2025; 38:1-18. [PMID: 39210806 PMCID: PMC11725728 DOI: 10.5713/ab.24.0291] [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: 05/01/2024] [Revised: 06/14/2024] [Accepted: 07/19/2024] [Indexed: 09/04/2024] Open
Abstract
The increase in methane emissions, a major greenhouse gas, threatens human well-being and global ecosystems due to its contribution to global warming. Livestock, particularly ruminants, have been a major research topic in recent decades due to their methane production. Therefore, the objective of the current review was to comprehensively discuss the in silico techniques used to mitigate methane production from ruminants. The review covers the principles of in silico docking and molecular dynamics, which can be used to develop methanogenesis inhibitors. It also discusses specific methanogen enzymes as potential targets for inhibitor development. Furthermore, in silico-based methanogenesis inhibitor development studies have been reviewed with the authors' opinions. The further use of in silico-based research techniques, including artificial intelligence-based systems, is encouraged to help reduce methane production from livestock more efficiently and costeffectively.
Collapse
Affiliation(s)
- Kamburawala Kankanamge Tharindu Namal Ranaweera
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
- Department of Animal Science, Faculty of Animal Science and Export Agriculture, Uva Wellassa University, Badulla 90000,
Sri Lanka
| | - Myunggi Baik
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
- Institute of Green-Bio Science and Technology, Seoul National University, Pyeongchang 25354,
Korea
| |
Collapse
|
5
|
Grabski H, Grabska S, Abagyan R. Identifying Allosteric Small-Molecule Binding Sites of Inactive NS2B-NS3 Proteases of Pathogenic Flaviviridae. Viruses 2024; 17:6. [PMID: 39861795 PMCID: PMC11769402 DOI: 10.3390/v17010006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2024] [Revised: 12/18/2024] [Accepted: 12/23/2024] [Indexed: 01/30/2025] Open
Abstract
Dengue, West Nile, Zika, Yellow fever, and Japanese encephalitis viruses persist as significant global health threats. The development of new therapeutic strategies based on inhibiting essential viral enzymes or viral-host protein interactions is problematic due to the fast mutation rate and rapid emergence of drug resistance. This study focuses on the NS2B-NS3 protease as a promising target for antiviral drug development. Promising allosteric binding sites were identified in two conformationally distinct inactive states and characterized for five flaviviruses and four Dengue virus subtypes. Their shapes, druggability, inter-viral similarity, sequence variation, and susceptibility to drug-resistant mutations have been studied. Two identified allosteric inactive state pockets appear to be feasible alternatives to a larger closed pocket near the active site, and they can be targeted with specific drug-like small-molecule inhibitors. Virus-specific sequence and structure implications and the feasibility of multi-viral inhibitors are discussed.
Collapse
Affiliation(s)
- Hovakim Grabski
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, CA 92093-0657, USA;
- L.A. Orbeli Institute of Physiology, National Academy of Sciences, Yerevan 0028, Armenia
| | - Siranuysh Grabska
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, CA 92093-0657, USA;
- L.A. Orbeli Institute of Physiology, National Academy of Sciences, Yerevan 0028, Armenia
| | - Ruben Abagyan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, CA 92093-0657, USA;
| |
Collapse
|
6
|
Natarajan A, Velmurugu Y, Becerra Flores M, Dibba F, Beesam S, Kikvadze S, Wang X, Wang W, Li T, Shin HW, Cardozo T, Krogsgaard M. In situ cell-surface conformation of the TCR-CD3 signaling complex. EMBO Rep 2024; 25:5719-5742. [PMID: 39511422 PMCID: PMC11624261 DOI: 10.1038/s44319-024-00314-3] [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: 12/30/2023] [Revised: 10/22/2024] [Accepted: 10/26/2024] [Indexed: 11/15/2024] Open
Abstract
The extracellular molecular organization of the individual CD3 subunits around the αβ T cell receptor (TCR) is critical for initiating T cell signaling. In this study, we incorporate photo-crosslinkers at specific sites within the TCRα, TCRβ, CD3δ, and CD3γ subunits. Through crosslinking and docking, we identify a CD3ε'-CD3γ-CD3ε-CD3δ arrangement situated around the αβTCR in situ within the cell surface environment. We demonstrate the importance of cholesterol in maintaining the stability of the complex and that the 'in situ' complex structure mirrors the structure from 'detergent-purified' complexes. In addition, mutations aimed at stabilizing extracellular TCR-CD3 interfaces lead to poor signaling, suggesting that subunit fluidity is indispensable for signaling. Finally, employing photo-crosslinking and CD3 tetramer assays, we show that the TCR-CD3 complex undergoes minimal subunit movements or reorientations upon interaction with activating antibodies and pMHC tetramers. This suggests an absence of 'inactive-active' conformational states in the TCR constant regions and the extracellular CD3 subunits, unlike the transmembrane regions of the complex. This study contributes a nuanced understanding of TCR signaling, which may inform the development of therapeutics for immune-related disorders.
Collapse
MESH Headings
- Signal Transduction
- CD3 Complex/chemistry
- CD3 Complex/metabolism
- Humans
- Receptor-CD3 Complex, Antigen, T-Cell/chemistry
- Receptor-CD3 Complex, Antigen, T-Cell/metabolism
- Receptor-CD3 Complex, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell, alpha-beta/chemistry
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Protein Conformation
- Cell Membrane/metabolism
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- Cholesterol/metabolism
- Cholesterol/chemistry
- Protein Binding
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Antigen, T-Cell/chemistry
- Protein Subunits/chemistry
- Protein Subunits/metabolism
- Models, Molecular
- Cross-Linking Reagents/chemistry
Collapse
Affiliation(s)
- Aswin Natarajan
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, 10016, USA
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Yogambigai Velmurugu
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, 10016, USA
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Manuel Becerra Flores
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Fatoumatta Dibba
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, 10016, USA
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Saikiran Beesam
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, 10016, USA
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Sally Kikvadze
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, 10016, USA
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Xiaotian Wang
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, 10016, USA
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Wenjuan Wang
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, 10016, USA
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Tianqi Li
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, 10016, USA
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Hye Won Shin
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, 10016, USA
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Timothy Cardozo
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Michelle Krogsgaard
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, 10016, USA.
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, 10016, USA.
| |
Collapse
|
7
|
Shi JJ, Liu YJ, Liu ZG, Chen RY, Wang R, Yu J, Li CY, Yang GJ, Chen J. Structure-Based identification of a potent KDM7A inhibitor exerts anticancer activity through transcriptionally reducing MKRN1 in taxol- resistant and -sensitive triple-negative breast cancer cells. Bioorg Chem 2024; 153:107945. [PMID: 39509788 DOI: 10.1016/j.bioorg.2024.107945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2024] [Revised: 10/26/2024] [Accepted: 11/03/2024] [Indexed: 11/15/2024]
Abstract
KDM7A, a histone demethylase implicated in cancer proliferation, metastasis, and drug resistance, represents a crucial therapeutic target. Utilizing "mcule.com" for virtual screening of 100,000 compounds from the ZINC database, we identified 12 compounds with high affinity for KDM7A, with compound 4 emerging as the leading candidate for effectively inhibiting KDM7A's demethylase activity. Analysis of the GTRD database, the Breast Cancer Gene Expression Miner website, and recent studies highlighted MKRN1, a gene associated with cell proliferation and drug resistance, as a key intersecting factor. Compared to 2,4-pyridine dicarboxylic acid, compound 4 significantly reduced breast cancer stem cells and induced G1 phase cell cycle arrest. Mechanistically, compound 4 inhibited KDM7A's binding to H3K27me3, decreased MKRN1 transcription, and increased the levels of cell cycle regulators p16, p21, and p27, while reducing stem cell markers ALDH1A1, CD44, and CD133. These findings suggest that compound 4 could serve as a promising lead for selective KDM7A-targeting drugs. Additionally, this study is the first to demonstrate MKRN1 as a downstream gene of KDM7A, showing significant inhibitory effects in both taxol-resistant and drug-sensitive triple-negative breast cancer (TNBC) cells. This research offers new insights into the anticancer mechanisms of KDM7A inhibitors and underscores KDM7A's potential as a therapeutic target against TNBC.
Collapse
Affiliation(s)
- Jin-Jin Shi
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo 315211, Zhejiang, China.
| | - Yan-Jun Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo 315211, Zhejiang, China.
| | - Zhi-Guo Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo 315211, Zhejiang, China.
| | - Ru-Yi Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo 315211, Zhejiang, China.
| | - Ran Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo 315211, Zhejiang, China.
| | - Jing Yu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo 315211, Zhejiang, China.
| | - Chang-Yun Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo 315211, Zhejiang, China.
| | - Guan-Jun Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo 315211, Zhejiang, China.
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo 315211, Zhejiang, China.
| |
Collapse
|
8
|
Cleves AE, Tandon H, Jain AN. Structure-based pose prediction: Non-cognate docking extended to macrocyclic ligands. J Comput Aided Mol Des 2024; 38:33. [PMID: 39414633 PMCID: PMC11485047 DOI: 10.1007/s10822-024-00574-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2024] [Accepted: 09/27/2024] [Indexed: 10/18/2024]
Abstract
So-called "cross-docking" is the prediction of the bound configuration of small-molecule ligands that differ from the cognate ligand of a protein co-crystal structure. This is a much more challenging problem than re-docking the cognate ligand, particularly when the new ligand is structurally dissimilar from prior known ones. We have updated the previously introduced PINC ("PINC Is Not Cognate") benchmark which introduced the idea of temporal segregation to measure cross-docking performance. The temporal set encompasses 846 future ligands for ten targets based on information from the earliest 25% of X-ray co-crystal structures known for each target. Here, we extend the benchmark to include thirteen targets where the bound poses of 128 macrocyclic ligands are to be predicted based on knowledge from structures of bound non-macrocyclic ligands. Performance was roughly equivalent for both the temporally-split non-macrocyclic ligand set and the macrocycle prediction set. Using standard and fully automatic protocols for the Surflex-Dock and ForceGen methods, across the combined 974 non-macrocyclic and macrocyclic ligands, the top-scoring pose family was correct 68% of the time, with the top-two pose families achieving a 79% success rate. Correct poses among all those predicted were identified 92% of the time. These success rates far exceeded those observed for the alternative methods AutoDock Vina and Gnina on both sets.
Collapse
Affiliation(s)
- Ann E Cleves
- BioPharmics Division, Optibrium Limited, Cambridge, CB25 9PB, UK
| | - Himani Tandon
- Research Department, Optibrium Limited, Cambridge, CB25 9PB, UK
| | - Ajay N Jain
- BioPharmics Division, Optibrium Limited, Cambridge, CB25 9PB, UK.
| |
Collapse
|
9
|
Ray P, Sedigh A, Confeld M, Alhalhooly L, Iduoku K, Casanola-Martin GM, Pham-The H, Rasulev B, Choi Y, Yang Z, Mallik S, Quadir M. Design and evaluation of nanoscale materials with programmed responsivity towards epigenetic enzymes. J Mater Chem B 2024; 12:9905-9920. [PMID: 39021201 DOI: 10.1039/d4tb00514g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Self-assembled materials capable of modulating their assembly properties in response to specific enzymes play a pivotal role in advancing 'intelligent' encapsulation platforms for biotechnological applications. Here, we introduce a previously unreported class of synthetic nanomaterials that programmatically interact with histone deacetylase (HDAC) as the triggering stimulus for disassembly. These nanomaterials consist of co-polypeptides comprising poly(acetyl L-lysine) and poly(ethylene glycol) blocks. Under neutral pH conditions, they self-assemble into particles. The hydrodynamic diameters of particles were typically withing the range of 108-190 nm, depending on degree of acetylation of the hydrophobic block. However, their stability is compromised upon exposure to HDACs, depending on enzyme concentration and exposure time. Our investigation, utilizing HDAC8 as the model enzyme, revealed that the primary mechanism behind disassembly involves a decrease in amphiphilicity within the block copolymer due to the deacetylation of lysine residues within the particles' hydrophobic domains. To elucidate the response mechanism, we encapsulated a fluorescent dye within these nanoparticles. Upon incubation with HDAC, the nanoparticle structure collapsed, leading to controlled release of the dye over time. Notably, this release was not triggered by denatured HDAC8, other proteolytic enzymes like trypsin, or the co-presence of HDAC8 and its inhibitor. We also demonstrated the biocompatibility and cellular effects of these materials in the context of drug delivery in different types of anticancer cell lines, such as MIA PaCa-2, PANC-1, cancer like stem cells (CSCs), and non-cancerous HPNE cells. We observed that the release of a model drug (such as a STAT3 pathway inhibitor, Napabucasin) can be loaded into these nanoparticles, with >90% of the dosage can be released over 3 h under the influence of HDAC8 enzyme in a controlled fashion. Further, we conducted a comprehensive computational study to unveil the possible interaction mechanism between enzymes and particles. By drawing parallels to the mechanism of naturally occurring histone proteins, this research represents a pioneering step toward developing functional materials capable of harnessing the activity of epigenetic enzymes such as HDACs.
Collapse
Affiliation(s)
- Priyanka Ray
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, ND 58102, USA.
| | - Abbas Sedigh
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, ND 58102, USA
| | - Matthew Confeld
- Deapartment of Physics, North Dakota State University, Fargo, ND 58102, USA
| | - Lina Alhalhooly
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58102, USA
| | - Kweeni Iduoku
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, ND 58102, USA.
| | - Gerardo M Casanola-Martin
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, ND 58102, USA.
| | - Hai Pham-The
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 10000, Vietnam
| | - Bakhtiyor Rasulev
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, ND 58102, USA.
| | - Yongki Choi
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58102, USA
| | - Zhongyu Yang
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, ND 58102, USA
| | - Sanku Mallik
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, ND 58102, USA
| | - Mohiuddin Quadir
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, ND 58102, USA.
| |
Collapse
|
10
|
Sorci L, Minazzato G, Amici A, Mazzola F, Raffaelli N. Periplasmic binding proteins Bug69 and Bug27 from Bordetella pertussis are in vitro high-affinity quinolinate binders with a potential role in NAD biosynthesis. FEBS Open Bio 2024; 14:1718-1730. [PMID: 39118291 PMCID: PMC11452294 DOI: 10.1002/2211-5463.13876] [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: 05/29/2024] [Revised: 07/22/2024] [Accepted: 07/30/2024] [Indexed: 08/10/2024] Open
Abstract
Bordetella's genome contains a large family of periplasmic binding proteins (PBPs) known as Bugs, whose functions are mainly unassigned. Two members, Bug27 and Bug69, have previously been considered potential candidates for the uptake of small pyridine precursors, possibly linked to NAD biosynthesis. Here, we show an in vitro affinity of Bug27 and Bug69 for quinolinate in the submicromolar range, with a marked preference over other NAD precursors. A combined sequence similarity network and genome context analysis identifies a cluster of Bug69/27 homologs that are genomically associated with the NAD transcriptional regulator NadQ and the enzyme quinolinate phosphoribosyltransferase (QaPRT, gene nadC), suggesting a functional linkage to NAD metabolism. Integrating molecular docking and structure-based multiple alignments confirms that quinolinate is the preferred ligand for Bug27 and Bug69.
Collapse
Affiliation(s)
- Leonardo Sorci
- Division of Bioinformatics and Biochemistry, Department of Science and Engineering of Matter, Environment and Urban PlanningPolytechnic University of MarcheAnconaItaly
| | - Gabriele Minazzato
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of MarcheAnconaItaly
| | - Adolfo Amici
- Department of Clinical SciencesPolytechnic University of MarcheAnconaItaly
| | - Francesca Mazzola
- Department of Clinical SciencesPolytechnic University of MarcheAnconaItaly
| | - Nadia Raffaelli
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of MarcheAnconaItaly
| |
Collapse
|
11
|
Shi S, Zheng Y, Goulding J, Marri S, Lucarini L, Konecny B, Sgambellone S, Villano S, Bosma R, Wijtmans M, Briddon SJ, Zarzycka BA, Vischer HF, Leurs R. A high-affinity, cis-on photoswitchable beta blocker to optically control β 2-adrenergic receptors in vitro and in vivo. Biochem Pharmacol 2024; 226:116396. [PMID: 38942089 DOI: 10.1016/j.bcp.2024.116396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/07/2024] [Accepted: 06/25/2024] [Indexed: 06/30/2024]
Abstract
This study introduces (S)-Opto-prop-2, a second-generation photoswitchable ligand designed for precise modulation of β2-adrenoceptor (β2AR). Synthesised by incorporating an azobenzene moiety with propranolol, (S)-Opto-prop-2 exhibited a high PSScis (photostationary state for cis isomer) percentage (∼90 %) and a favourable half-life (>10 days), facilitating diverse bioassay measurements. In vitro, the cis-isomer displayed substantially higher β2AR binding affinity than the trans-isomer (1000-fold), making (S)-Opto-prop-2 one of the best photoswitchable GPCR (G protein-coupled receptor) ligands reported so far. Molecular docking of (S)-Opto-prop-2 in the X-ray structure of propranolol-bound β2AR followed by site-directed mutagenesis studies, identified D1133.32, N3127.39 and F2896.51 as crucial residues that contribute to ligand-receptor interactions at the molecular level. In vivo efficacy was assessed using a rabbit ocular hypertension model, revealing that the cis isomer mimicked propranolol's effects in reducing intraocular pressure, while the trans isomer was inactive. Dynamic optical modulation of β2AR by (S)-Opto-prop-2 was demonstrated in two different cAMP bioassays and using live-cell confocal imaging, indicating reversible and dynamic control of β2AR activity using the new photopharmacology tool. In conclusion, (S)-Opto-prop-2 emerges as a promising photoswitchable ligand for precise and reversible β2AR modulation with light. The new tool shows superior cis-on binding affinity, one of the largest reported differences in affinity (1000-fold) between its two configurations, in vivo efficacy, and dynamic modulation. This study contributes valuable insights into the evolving field of photopharmacology, offering a potential avenue for targeted therapy in β2AR-associated pathologies.
Collapse
Affiliation(s)
- Shuang Shi
- Division of Medicinal Chemistry, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, 1081HZ Amsterdam, the Netherlands
| | - Yang Zheng
- Division of Medicinal Chemistry, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, 1081HZ Amsterdam, the Netherlands
| | - Joëlle Goulding
- Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, The Midlands NG7 2UH, U.K; Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, U.K
| | - Silvia Marri
- Department of Neurosciences, Psychology, Drug Research and Child Health (NEUROFARBA), University of Florence, Florence, 50139, Italy
| | - Laura Lucarini
- Department of Neurosciences, Psychology, Drug Research and Child Health (NEUROFARBA), University of Florence, Florence, 50139, Italy
| | - Benjamin Konecny
- Division of Medicinal Chemistry, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, 1081HZ Amsterdam, the Netherlands
| | - Silvia Sgambellone
- Department of Neurosciences, Psychology, Drug Research and Child Health (NEUROFARBA), University of Florence, Florence, 50139, Italy
| | - Serafina Villano
- Department of Neurosciences, Psychology, Drug Research and Child Health (NEUROFARBA), University of Florence, Florence, 50139, Italy
| | - Reggie Bosma
- Division of Medicinal Chemistry, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, 1081HZ Amsterdam, the Netherlands
| | - Maikel Wijtmans
- Division of Medicinal Chemistry, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, 1081HZ Amsterdam, the Netherlands
| | - Stephen J Briddon
- Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, The Midlands NG7 2UH, U.K; Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, U.K
| | - Barbara A Zarzycka
- Division of Medicinal Chemistry, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, 1081HZ Amsterdam, the Netherlands
| | - Henry F Vischer
- Division of Medicinal Chemistry, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, 1081HZ Amsterdam, the Netherlands
| | - Rob Leurs
- Division of Medicinal Chemistry, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, 1081HZ Amsterdam, the Netherlands.
| |
Collapse
|
12
|
Aboul Hosn S, El Ahmadieh C, Thoumi S, Sinno A, Al Khoury C. Cimicifugoside H-2 as an Inhibitor of IKK1/Alpha: A Molecular Docking and Dynamic Simulation Study. Biomolecules 2024; 14:860. [PMID: 39062574 PMCID: PMC11274867 DOI: 10.3390/biom14070860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 06/23/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024] Open
Abstract
One of the most challenging issues scientists face is finding a suitable non-invasive treatment for cancer, as it is widespread around the world. The efficacy of phytochemicals that target oncogenic pathways appears to be quite promising and has gained attention over the past few years. We investigated the effect of docking phytochemicals isolated from the rhizomes of the Cimicifuga foetida plant on different domains of the IκB kinase alpha (IKK1/alpha) protein. The Cimicifugoside H-2 phytochemical registered a high docking score on the activation loop of IKK1/alpha amongst the other phytochemicals compared to the positive control. The interaction of the protein with Cimicifugoside H-2 was mostly stabilized by hydrogen bonds and hydrophobic interactions. A dynamic simulation was then performed with the Cimicifugoside H-2 phytochemical on the activation loop of IKK1/alpha, revealing that Cimicifugoside H-2 is a possible inhibitor of this protein. The pharmacokinetic properties of the drug were also examined to assess the safety of administering the drug. Therefore, in this in silico study, we discovered that the Cimicifugoside H-2 phytochemical inhibits the actively mutated conformation of IKK1/alpha, potentially suppressing the nuclear factor kappa light chain enhancer of activated B cells (NF-κB) pathway.
Collapse
Affiliation(s)
- Shahd Aboul Hosn
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Beirut Campus, P.O. Box 13-5053, Chouran, Beirut 1102 2801, Lebanon (C.E.A.)
| | - Christina El Ahmadieh
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Beirut Campus, P.O. Box 13-5053, Chouran, Beirut 1102 2801, Lebanon (C.E.A.)
| | - Sergio Thoumi
- Department of Computer Science and Mathematics, Lebanese American University, Beirut Campus, P.O. Box 13-5053, Chouran, Beirut 1102 2801, Lebanon
| | - Aia Sinno
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Beirut Campus, P.O. Box 13-5053, Chouran, Beirut 1102 2801, Lebanon (C.E.A.)
| | - Charbel Al Khoury
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Beirut Campus, P.O. Box 13-5053, Chouran, Beirut 1102 2801, Lebanon (C.E.A.)
| |
Collapse
|
13
|
Matteucci F, Ferrati M, Spinozzi E, Piergentili A, Del Bello F, Giorgioni G, Sorci L, Petrelli R, Cappellacci L. Synthesis, Biological, and Computational Evaluations of Conformationally Restricted NAD-Mimics as Discriminant Inhibitors of Human NMN-Adenylyltransferase Isozymes. Pharmaceuticals (Basel) 2024; 17:739. [PMID: 38931406 PMCID: PMC11207052 DOI: 10.3390/ph17060739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 05/27/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024] Open
Abstract
Nicotinamide adenine dinucleotide (NAD) cofactor metabolism plays a significant role in cancer development. Tumor cells have an increased demand for NAD and ATP to support rapid growth and proliferation. Limiting the amount of available NAD by targeting critical NAD biosynthesis enzymes has emerged as a promising anticancer therapeutic approach. In mammals, the enzyme nicotinamide/nicotinic acid adenylyltransferase (NMNAT) catalyzes a crucial downstream reaction for all known NAD synthesis routes. Novel nicotinamide/nicotinic acid adenine dinucleotide (NAD/NaAD) analogues 1-4, containing a methyl group at the ribose 2'-C and 3'-C-position of the adenosine moiety, were synthesized as inhibitors of the three isoforms of human NMN-adenylyltransferase, named hNMNAT-1, hNMNAT-2, and hNMNAT-3. An NMR-based conformational analysis suggests that individual NAD-analogues (1-4) have distinct conformational preferences. Biological evaluation of dinucleotides 1-4 as inhibitors of hNMNAT isoforms revealed structural relationships between different conformations (North-anti and South-syn) and enzyme-inhibitory activity. Among the new series of NAD analogues synthesized and tested, the 2'-C-methyl-NAD analogue 1 (Ki = 15 and 21 µM towards NMN and ATP, respectively) emerged as the most potent and selective inhibitor of hNMNAT-2 reported so far. Finally, we rationalized the in vitro bioactivity and selectivity of methylated NAD analogues with in silico studies, helping to lay the groundwork for rational scaffold optimization.
Collapse
Affiliation(s)
- Federica Matteucci
- Medicinal Chemistry Unit, School of Pharmacy, Chemistry Interdisciplinary Project (ChIP), University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy; (F.M.); (M.F.); (E.S.); (A.P.); (F.D.B.); (G.G.); (L.C.)
| | - Marta Ferrati
- Medicinal Chemistry Unit, School of Pharmacy, Chemistry Interdisciplinary Project (ChIP), University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy; (F.M.); (M.F.); (E.S.); (A.P.); (F.D.B.); (G.G.); (L.C.)
| | - Eleonora Spinozzi
- Medicinal Chemistry Unit, School of Pharmacy, Chemistry Interdisciplinary Project (ChIP), University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy; (F.M.); (M.F.); (E.S.); (A.P.); (F.D.B.); (G.G.); (L.C.)
| | - Alessia Piergentili
- Medicinal Chemistry Unit, School of Pharmacy, Chemistry Interdisciplinary Project (ChIP), University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy; (F.M.); (M.F.); (E.S.); (A.P.); (F.D.B.); (G.G.); (L.C.)
| | - Fabio Del Bello
- Medicinal Chemistry Unit, School of Pharmacy, Chemistry Interdisciplinary Project (ChIP), University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy; (F.M.); (M.F.); (E.S.); (A.P.); (F.D.B.); (G.G.); (L.C.)
| | - Gianfabio Giorgioni
- Medicinal Chemistry Unit, School of Pharmacy, Chemistry Interdisciplinary Project (ChIP), University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy; (F.M.); (M.F.); (E.S.); (A.P.); (F.D.B.); (G.G.); (L.C.)
| | - Leonardo Sorci
- Division of Bioinformatics and Biochemistry, Department of Science and Engineering of Matter, Environment and Urban Planning (SIMAU), Polytechnic University of Marche, 60131 Ancona, Italy
| | - Riccardo Petrelli
- Medicinal Chemistry Unit, School of Pharmacy, Chemistry Interdisciplinary Project (ChIP), University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy; (F.M.); (M.F.); (E.S.); (A.P.); (F.D.B.); (G.G.); (L.C.)
| | - Loredana Cappellacci
- Medicinal Chemistry Unit, School of Pharmacy, Chemistry Interdisciplinary Project (ChIP), University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy; (F.M.); (M.F.); (E.S.); (A.P.); (F.D.B.); (G.G.); (L.C.)
| |
Collapse
|
14
|
Al Khoury C, Thoumi S, Tokajian S, Sinno A, Nemer G, El Beyrouthy M, Rahy K. ABC transporter inhibition by beauvericin partially overcomes drug resistance in Leishmania tropica. Antimicrob Agents Chemother 2024; 68:e0136823. [PMID: 38572959 PMCID: PMC11064568 DOI: 10.1128/aac.01368-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 03/15/2024] [Indexed: 04/05/2024] Open
Abstract
Leishmaniasis is a neglected tropical disease infecting the world's poorest populations. Miltefosine (ML) remains the primary oral drug against the cutaneous form of leishmaniasis. The ATP-binding cassette (ABC) transporters are key players in the xenobiotic efflux, and their inhibition could enhance the therapeutic index. In this study, the ability of beauvericin (BEA) to overcome ABC transporter-mediated resistance of Leishmania tropica to ML was assessed. In addition, the transcription profile of genes involved in resistance acquisition to ML was inspected. Finally, we explored the efflux mechanism of the drug and inhibitor. The efficacy of ML against all developmental stages of L. tropica in the presence or absence of BEA was evaluated using an absolute quantification assay. The expression of resistance genes was evaluated, comparing susceptible and resistant strains. Finally, the mechanisms governing the interaction between the ABC transporter and its ligands were elucidated using molecular docking and dynamic simulation. Relative quantification showed that the expression of the ABCG sub-family is mostly modulated by ML. In this study, we used BEA to impede resistance of Leishmania tropica. The IC50 values, following BEA treatment, were significantly reduced from 30.83, 48.17, and 16.83 µM using ML to 8.14, 11.1, and 7.18 µM when using a combinatorial treatment (ML + BEA) against promastigotes, axenic amastigotes, and intracellular amastigotes, respectively. We also demonstrated a favorable BEA-binding enthalpy to L. tropica ABC transporter compared to ML. Our study revealed that BEA partially reverses the resistance development of L. tropica to ML by blocking the alternate ATP hydrolysis cycle.
Collapse
Affiliation(s)
- Charbel Al Khoury
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Beirut, Lebanon
| | - Sergio Thoumi
- Department of Computer Science and Mathematics, Lebanese American University, Beirut, Lebanon
| | - Sima Tokajian
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon
| | - Aia Sinno
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Beirut, Lebanon
| | - Georges Nemer
- Division of Genomics and Translational Biomedicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Mark El Beyrouthy
- Department of Agriculture and Food Engineering, Holy Spirit University of Kaslik, Jounieh, Lebanon
| | - Kelven Rahy
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon
| |
Collapse
|
15
|
Mslati H, Gentile F, Pandey M, Ban F, Cherkasov A. PROTACable Is an Integrative Computational Pipeline of 3-D Modeling and Deep Learning To Automate the De Novo Design of PROTACs. J Chem Inf Model 2024; 64:3034-3046. [PMID: 38504115 DOI: 10.1021/acs.jcim.3c01878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Proteolysis-targeting chimeras (PROTACs) that engage two biological targets at once are a promising technology in degrading clinically relevant protein targets. Since factors that influence the biological activities of PROTACs are more complex than those of a small molecule drug, we explored a combination of computational chemistry and deep learning strategies to forecast PROTAC activity and enable automated design. A new method named PROTACable was developed for the de novo design of PROTACs, which includes a robust 3-D modeling workflow to model PROTAC ternary complexes using a library of E3 ligase and linker and an SE(3)-equivariant graph transformer network to predict the activity of newly designed PROTACs. PROTACable is available at https://github.com/giaguaro/PROTACable/.
Collapse
Affiliation(s)
- Hazem Mslati
- Vancouver Prostate Centre, The University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada
| | - Francesco Gentile
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
- Ottawa Institute of Systems Biology, Ottawa, Ontario K1N 6N5, Canada
| | - Mohit Pandey
- Vancouver Prostate Centre, The University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada
| | - Fuqiang Ban
- Vancouver Prostate Centre, The University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada
| | - Artem Cherkasov
- Vancouver Prostate Centre, The University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada
| |
Collapse
|
16
|
Overduin M, Bhat R. Recognition and remodeling of endosomal zones by sorting nexins. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184305. [PMID: 38408696 DOI: 10.1016/j.bbamem.2024.184305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 02/05/2024] [Accepted: 02/18/2024] [Indexed: 02/28/2024]
Abstract
The proteolipid code determines how cytosolic proteins find and remodel membrane surfaces. Here, we investigate how this process works with sorting nexins Snx1 and Snx3. Both proteins form sorting machines by recognizing membrane zones enriched in phosphatidylinositol 3-phosphate (PI3P), phosphatidylserine (PS) and cholesterol. This co-localized combination forms a unique "lipid codon" or lipidon that we propose is responsible for endosomal targeting, as revealed by structures and interactions of their PX domain-based readers. We outline a membrane recognition and remodeling mechanism for Snx1 and Snx3 involving this code element alongside transmembrane pH gradients, dipole moment-guided docking and specific protein-protein interactions. This generates an initial membrane-protein assembly (memtein) that then recruits retromer and additional PX proteins to recruit cell surface receptors for sorting to the trans-Golgi network (TGN), lysosome and plasma membranes. Post-translational modification (PTM) networks appear to regulate how the sorting machines form and operate at each level. The commonalities and differences between these sorting nexins show how the proteolipid code orchestrates parallel flows of molecular information from ribosome emergence to organelle genesis, and illuminates a universally applicable model of the membrane.
Collapse
Affiliation(s)
- Michael Overduin
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada.
| | - Rakesh Bhat
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| |
Collapse
|
17
|
Hendi NN, Nemer G. In silico characterization of the novel SDR42E1 as a potential vitamin D modulator. J Steroid Biochem Mol Biol 2024; 238:106447. [PMID: 38160768 DOI: 10.1016/j.jsbmb.2023.106447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 01/03/2024]
Abstract
The short-chain dehydrogenase/reductase (SDR) superfamily encompasses enzymes that play essential roles in the metabolism of steroid hormones and lipids. Despite an enigmatic function, recent genetic studies have linked the novel SDR 42 extended-1 (SDR42E1) gene to 25-hydroxyvitamin D levels. This study investigated the potential SDR42E1 functions and interactions with vitamin D using bioinformatics and molecular docking studies. Phylogenetic analysis unveiled that the nucleotide sequences of human SDR42E1 exhibit high evolutionary conservation across nematodes and fruit flies. Molecular docking analysis identified strong binding affinities between SDR42E1 and its orthologs with vitamin D3 and essential precursors, 8-dehydrocholesterol, followed by 7-dehydrocholesterol and 25-hydroxyvitamin D. The hydrophobic interactions observed between the protein residues and vitamin D compounds supported the predicted transmembrane localization of SDR42E1. Our investigation provides valuable insights into the potential role of SDR42E1 in skin vitamin D biosynthesis throughout species. This provides the foundation for future research and development of targeted therapies for vitamin D deficiency and related health conditions.
Collapse
Affiliation(s)
- Nagham Nafiz Hendi
- Division of Genomics and Translational Biomedicine, College of Health and Life Sciences, Hamad Bin Khalifa University, P.O. Box 34110, Doha, Qatar
| | - Georges Nemer
- Division of Genomics and Translational Biomedicine, College of Health and Life Sciences, Hamad Bin Khalifa University, P.O. Box 34110, Doha, Qatar; Department of Biochemistry and Molecular Genetics, American University of Beirut, P.O. Box 110236, Beirut, Lebanon.
| |
Collapse
|
18
|
Ray P, Sedigh A, Confeld M, Alhalhooly L, Iduoku K, Casanola-Martin GM, Pham-The H, Rasulev B, Choi Y, Yang Z, Mallik S, Quadir M. Design and Evaluation of Nanoscale Materials with Programmed Responsivity towards Epigenetic Enzymes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.26.585429. [PMID: 38586020 PMCID: PMC10996597 DOI: 10.1101/2024.03.26.585429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Self-assembled materials capable of modulating their assembly properties in response to specific enzymes play a pivotal role in advancing 'intelligent' encapsulation platforms for biotechnological applications. Here, we introduce a previously unreported class of synthetic nanomaterials that programmatically interact with histone deacetylase (HDAC) as the triggering stimulus for disassembly. These nanomaterials consist of co-polypeptides comprising poly (acetyl L-lysine) and poly(ethylene glycol) blocks. Under neutral pH conditions, they self-assemble into particles. However, their stability is compromised upon exposure to HDACs, depending on enzyme concentration and exposure time. Our investigation, utilizing HDAC8 as the model enzyme, revealed that the primary mechanism behind disassembly involves a decrease in amphiphilicity within the block copolymer due to the deacetylation of lysine residues within the particles' hydrophobic domains. To elucidate the response mechanism, we encapsulated a fluorescent dye within these nanoparticles. Upon incubation with HDAC, the nanoparticle structure collapsed, leading to controlled release of the dye over time. Notably, this release was not triggered by denatured HDAC8, other proteolytic enzymes like trypsin, or the co-presence of HDAC8 and its inhibitor. We further demonstrated the biocompatibility and cellular effects of these materials and conducted a comprehensive computational study to unveil the possible interaction mechanism between enzymes and particles. By drawing parallels to the mechanism of naturally occurring histone proteins, this research represents a pioneering step toward developing functional materials capable of harnessing the activity of epigenetic enzymes such as HDACs.
Collapse
|
19
|
Zarca AM, Adlere I, Viciano CP, Arimont-Segura M, Meyrath M, Simon IA, Bebelman JP, Laan D, Custers HGJ, Janssen E, Versteegh KL, Buzink MCML, Nesheva DN, Bosma R, de Esch IJP, Vischer HF, Wijtmans M, Szpakowska M, Chevigné A, Hoffmann C, de Graaf C, Zarzycka BA, Windhorst AD, Smit MJ, Leurs R. Pharmacological Characterization and Radiolabeling of VUF15485, a High-Affinity Small-Molecule Agonist for the Atypical Chemokine Receptor ACKR3. Mol Pharmacol 2024; 105:301-312. [PMID: 38346795 DOI: 10.1124/molpharm.123.000835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/16/2024] [Indexed: 03/16/2024] Open
Abstract
Atypical chemokine receptor 3 (ACKR3), formerly referred to as CXCR7, is considered to be an interesting drug target. In this study, we report on the synthesis, pharmacological characterization and radiolabeling of VUF15485, a new ACKR3 small-molecule agonist, that will serve as an important new tool to study this β-arrestin-biased chemokine receptor. VUF15485 binds with nanomolar affinity (pIC50 = 8.3) to human ACKR3, as measured in [125I]CXCL12 competition binding experiments. Moreover, in a bioluminescence resonance energy transfer-based β-arrestin2 recruitment assay VUF15485 acts as a potent ACKR3 agonist (pEC50 = 7.6) and shows a similar extent of receptor activation compared with CXCL12 when using a newly developed, fluorescence resonance energy transfer-based ACKR3 conformational sensor. Moreover, the ACKR3 agonist VUF15485, tested against a (atypical) chemokine receptor panel (agonist and antagonist mode), proves to be selective for ACKR3. VUF15485 labeled with tritium at one of its methoxy groups ([3H]VUF15485), binds ACKR3 saturably and with high affinity (K d = 8.2 nM). Additionally, [3H]VUF15485 shows rapid binding kinetics and consequently a short residence time (<2 minutes) for binding to ACKR3. The selectivity of [3H]VUF15485 for ACKR3, was confirmed by binding studies, whereupon CXCR3, CXCR4, and ACKR3 small-molecule ligands were competed for binding against the radiolabeled agonist. Interestingly, the chemokine ligands CXCL11 and CXCL12 are not able to displace the binding of [3H]VUF15485 to ACKR3. The radiolabeled VUF15485 was subsequently used to evaluate its binding pocket. Site-directed mutagenesis and docking studies using a recently solved cryo-EM structure propose that VUF15485 binds in the major and the minor binding pocket of ACKR3. SIGNIFICANCE STATEMENT: The atypical chemokine receptor atypical chemokine receptor 3 (ACKR3) is considered an interesting drug target in relation to cancer and multiple sclerosis. The study reports on new chemical biology tools for ACKR3, i.e., a new agonist that can also be radiolabeled and a new ACKR3 conformational sensor, that both can be used to directly study the interaction of ACKR3 ligands with the G protein-coupled receptor.
Collapse
Affiliation(s)
- Aurelien M Zarca
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Ilze Adlere
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Cristina P Viciano
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Marta Arimont-Segura
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Max Meyrath
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Icaro A Simon
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Jan Paul Bebelman
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Dennis Laan
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Hans G J Custers
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Elwin Janssen
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Kobus L Versteegh
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Maurice C M L Buzink
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Desislava N Nesheva
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Reggie Bosma
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Iwan J P de Esch
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Henry F Vischer
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Maikel Wijtmans
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Martyna Szpakowska
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Andy Chevigné
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Carsten Hoffmann
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Chris de Graaf
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Barbara A Zarzycka
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Albert D Windhorst
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Martine J Smit
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Rob Leurs
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| |
Collapse
|
20
|
Chidambara Thanu V, Jabeen A, Ranganathan S. iBio-GATS-A Semi-Automated Workflow for Structural Modelling of Insect Odorant Receptors. Int J Mol Sci 2024; 25:3055. [PMID: 38474300 DOI: 10.3390/ijms25053055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 02/26/2024] [Accepted: 03/04/2024] [Indexed: 03/14/2024] Open
Abstract
Insects utilize seven transmembrane (7TM) odorant receptor (iOR) proteins, with an inverted topology compared to G-protein coupled receptors (GPCRs), to detect chemical cues in the environment. For pest biocontrol, chemical attractants are used to trap insect pests. However, with the influx of invasive insect pests, novel odorants are urgently needed, specifically designed to match 3D iOR structures. Experimental structural determination of these membrane receptors remains challenging and only four experimental iOR structures from two evolutionarily distant organisms have been solved. Template-based modelling (TBM) is a complementary approach, to generate model structures, selecting templates based on sequence identity. As the iOR family is highly divergent, a different template selection approach than sequence identity is needed. Bio-GATS template selection for GPCRs, based on hydrophobicity correspondence, has been morphed into iBio-GATS, for template selection from available experimental iOR structures. This easy-to-use semi-automated workflow has been extended to generate high-quality models from any iOR sequence from the selected template, using Python and shell scripting. This workflow was successfully validated on Apocrypta bakeri Orco and Machilis hrabei OR5 structures. iBio-GATS models generated for the fruit fly iOR, OR59b and Orco, yielded functional ligand binding results concordant with experimental mutagenesis findings, compared to AlphaFold2 models.
Collapse
Affiliation(s)
| | - Amara Jabeen
- Applied Biosciences, Macquarie University, Sydney 2109, Australia
| | | |
Collapse
|
21
|
Dehghani-Ghahnaviyeh S, Soylu C, Furet P, Velez-Vega C. Dissecting the Interaction Fingerprints and Binding Affinity of BYL719 Analogs Targeting PI3Kα. J Phys Chem B 2024; 128:1819-1829. [PMID: 38373112 DOI: 10.1021/acs.jpcb.3c06766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Phosphatidylinositol-3-kinase Alpha (PI3Kα) is a lipid kinase which regulates signaling pathways involved in cell proliferation. Dysregulation of these pathways promotes several human cancers, pushing for the development of anticancer drugs to target PI3Kα. One such medicinal chemistry campaign at Novartis led to the discovery of BYL719 (Piqray, Alpelicib), a PI3Kα inhibitor approved by the FDA in 2019 for treatment of HR+/HER2-advanced breast cancer with a PIK3CA mutation. Structure-based drug design played a key role in compound design and optimization throughout the discovery process. However, further characterization of potency drivers via structural dynamics and energetic analyses can be advantageous for ensuing PI3Kα programs. Here, our goal is to employ various in-silico techniques, including molecular simulations and machine learning, to characterize 14 ligands from the BYL719 analogs and predict their binding affinities. The structural insights from molecular simulations suggest that although the ligand-hinge interaction is the primary driver of ligand stability at the pocket, the R group positioning at C2 or C6 of pyridine/pyrimidine also plays a major role. Binding affinities predicted via thermodynamic integration (TI) are in good agreement with previously reported IC50s. Yet, computationally demanding techniques such as TI might not always be the most efficient approach for affinity prediction, as in our case study, fast high-throughput techniques were capable of classifying compounds as active or inactive, and one docking approach showed accuracy comparable to TI.
Collapse
Affiliation(s)
- Sepehr Dehghani-Ghahnaviyeh
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Cihan Soylu
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Pascal Furet
- Novartis Institutes for BioMedical Research, CH4002 Basel, Switzerland
| | - Camilo Velez-Vega
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
22
|
Dawson JRD, Wadman GM, Zhang P, Tebben A, Carter PH, Gu S, Shroka T, Borrega-Roman L, Salanga CL, Handel TM, Kufareva I. Molecular determinants of antagonist interactions with chemokine receptors CCR2 and CCR5. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.15.567150. [PMID: 38014122 PMCID: PMC10680698 DOI: 10.1101/2023.11.15.567150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
By driving monocyte chemotaxis, the chemokine receptor CCR2 shapes inflammatory responses and the formation of tumor microenvironments. This makes it a promising target in inflammation and immuno-oncology; however, despite extensive efforts, there are no FDA-approved CCR2-targeting therapeutics. Cited challenges include the redundancy of the chemokine system, suboptimal properties of compound candidates, and species differences that confound the translation of results from animals to humans. Structure-based drug design can rationalize and accelerate the discovery and optimization of CCR2 antagonists to address these challenges. The prerequisites for such efforts include an atomic-level understanding of the molecular determinants of action of existing antagonists. In this study, using molecular docking and artificial-intelligence-powered compound library screening, we uncover the structural principles of small molecule antagonism and selectivity towards CCR2 and its sister receptor CCR5. CCR2 orthosteric inhibitors are shown to universally occupy an inactive-state-specific tunnel between receptor helices 1 and 7; we also discover an unexpected role for an extra-helical groove accessible through this tunnel, suggesting its potential as a new targetable interface for CCR2 and CCR5 modulation. By contrast, only shape complementarity and limited helix 8 hydrogen bonding govern the binding of various chemotypes of allosteric antagonists. CCR2 residues S1012.63 and V2446.36 are implicated as determinants of CCR2/CCR5 and human/mouse orthosteric and allosteric antagonist selectivity, respectively, and the role of S1012.63 is corroborated through experimental gain-of-function mutagenesis. We establish a critical role of induced fit in antagonist recognition, reveal strong chemotype selectivity of existing structures, and demonstrate the high predictive potential of a new deep-learning-based compound scoring function. Finally, this study expands the available CCR2 structural landscape with computationally generated chemotype-specific models well-suited for structure-based antagonist design.
Collapse
Affiliation(s)
- John R D Dawson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Grant M Wadman
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | | | | | - Percy H Carter
- Bristol Myers Squibb Company, Princeton, NJ, USA
- (current affiliation) Blueprint Medicines, Cambridge, MA, USA
| | - Siyi Gu
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- (current affiliation) Lycia Therapeutics, South San Francisco, CA
| | - Thomas Shroka
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- (current affiliation) Avidity Biosciences Inc., San Diego, CA
| | - Leire Borrega-Roman
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Catherina L Salanga
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Tracy M Handel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Irina Kufareva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| |
Collapse
|
23
|
Sulimov AV, Ilin IS, Tashchilova AS, Kondakova OA, Kutov DC, Sulimov VB. Docking and other computing tools in drug design against SARS-CoV-2. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2024; 35:91-136. [PMID: 38353209 DOI: 10.1080/1062936x.2024.2306336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/10/2024] [Indexed: 02/16/2024]
Abstract
The use of computer simulation methods has become an indispensable component in identifying drugs against the SARS-CoV-2 coronavirus. There is a huge body of literature on application of molecular modelling to predict inhibitors against target proteins of SARS-CoV-2. To keep our review clear and readable, we limited ourselves primarily to works that use computational methods to find inhibitors and test the predicted compounds experimentally either in target protein assays or in cell culture with live SARS-CoV-2. Some works containing results of experimental discovery of corresponding inhibitors without using computer modelling are included as examples of a success. Also, some computational works without experimental confirmations are also included if they attract our attention either by simulation methods or by databases used. This review collects studies that use various molecular modelling methods: docking, molecular dynamics, quantum mechanics, machine learning, and others. Most of these studies are based on docking, and other methods are used mainly for post-processing to select the best compounds among those found through docking. Simulation methods are presented concisely, information is also provided on databases of organic compounds that can be useful for virtual screening, and the review itself is structured in accordance with coronavirus target proteins.
Collapse
Affiliation(s)
- A V Sulimov
- Dimonta Ltd., Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
| | - I S Ilin
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
| | - A S Tashchilova
- Dimonta Ltd., Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
| | - O A Kondakova
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
| | - D C Kutov
- Dimonta Ltd., Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
| | - V B Sulimov
- Dimonta Ltd., Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
| |
Collapse
|
24
|
Platonov M, Maximyuk O, Rayevsky A, Iegorova O, Hurmach V, Holota Y, Bulgakov E, Cherninskyi A, Karpov P, Ryabukhin S, Krishtal O, Volochnyuk D. Integrated workflow for the identification of new GABA A R positive allosteric modulators based on the in silico screening with further in vitro validation. Case study using Enamine's stock chemical space. Mol Inform 2024; 43:e202300156. [PMID: 37964718 DOI: 10.1002/minf.202300156] [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: 06/11/2023] [Revised: 11/10/2023] [Accepted: 11/14/2023] [Indexed: 11/16/2023]
Abstract
Numerous studies reported an association between GABAA R subunit genes and epilepsy, eating disorders, autism spectrum disorders, neurodevelopmental disorders, and bipolar disorders. This study was aimed to find some potential positive allosteric modulators and was performed by combining the in silico approach with further in vitro evaluation of its real activity. We started from the GABAA R-diazepam complexes and assembled a lipid embedded protein ensemble to refine it via molecular dynamics (MD) simulation. Then we focused on the interaction of α1β2γ2 with some Z-drugs (non-benzodiazepine compounds) using an Induced Fit Docking (IFD) into the relaxed binding site to generate a pharmacophore model. The pharmacophore model was validated with a reference set and applied to decrease the pre-filtered Enamine database before the main docking procedure. Finally, we succeeded in identifying a set of compounds, which met all features of the docking model. The aqueous solubility and stability of these compounds in mouse plasma were assessed. Then they were tested for the biological activity using the rat Purkinje neurons and CHO cells with heterologously expressed human α1β2γ2 GABAA receptors. Whole-cell patch clamp recordings were used to reveal the GABA induced currents. Our study represents a convenient and tunable model for the discovery of novel positive allosteric modulators of GABAA receptors. A High-throughput virtual screening of the largest available database of chemical compounds resulted in the selection of 23 compounds. Further electrophysiological tests allowed us to determine a set of 3 the most outstanding active compounds. Considering the structural features of leader compounds, the study can develop into the MedChem project soon.
Collapse
Affiliation(s)
- Maksym Platonov
- Institute of molecular biology and genetics, Natl. Academy of Sciences of Ukraine, Zabolotnogo Str., 150, Kyiv, 03143, Ukraine
- Enamine Ltd., 78 Chervonotkatska Str., 02660, Kyiv, Ukraine
| | - Oleksandr Maximyuk
- Bogomoletz Institute of Physiology, Natl. Academy of Sciences of Ukraine, 4 Bogomoletz Str., 01024, Kyiv, Ukraine
| | - Alexey Rayevsky
- Institute of molecular biology and genetics, Natl. Academy of Sciences of Ukraine, Zabolotnogo Str., 150, Kyiv, 03143, Ukraine
- Enamine Ltd., 78 Chervonotkatska Str., 02660, Kyiv, Ukraine
- Institute of Food Biotechnology and Genomics, Natl. Academy of Sciences of Ukraine, Osypovskoho Str., 2 A, Kyiv, 04123, Ukraine
| | - Olena Iegorova
- Bogomoletz Institute of Physiology, Natl. Academy of Sciences of Ukraine, 4 Bogomoletz Str., 01024, Kyiv, Ukraine
| | - Vasyl Hurmach
- Institute of molecular biology and genetics, Natl. Academy of Sciences of Ukraine, Zabolotnogo Str., 150, Kyiv, 03143, Ukraine
- Enamine Ltd., 78 Chervonotkatska Str., 02660, Kyiv, Ukraine
| | - Yuliia Holota
- Enamine Ltd., 78 Chervonotkatska Str., 02660, Kyiv, Ukraine
| | - Elijah Bulgakov
- Enamine Ltd., 78 Chervonotkatska Str., 02660, Kyiv, Ukraine
- Institute of Food Biotechnology and Genomics, Natl. Academy of Sciences of Ukraine, Osypovskoho Str., 2 A, Kyiv, 04123, Ukraine
| | - Andrii Cherninskyi
- Bogomoletz Institute of Physiology, Natl. Academy of Sciences of Ukraine, 4 Bogomoletz Str., 01024, Kyiv, Ukraine
| | - Pavel Karpov
- Institute of Food Biotechnology and Genomics, Natl. Academy of Sciences of Ukraine, Osypovskoho Str., 2 A, Kyiv, 04123, Ukraine
| | - Sergey Ryabukhin
- Enamine Ltd., 78 Chervonotkatska Str., 02660, Kyiv, Ukraine
- Institute of High Technologies, Taras Shevchenko National University of Kyiv., Glushkova Ave, 03022, Kyiv, Ukraine
- Institute of organic chemistry NAS of Ukraine, 5 Murmanska Str., 02660, Kyiv, Ukraine
| | - Oleg Krishtal
- Bogomoletz Institute of Physiology, Natl. Academy of Sciences of Ukraine, 4 Bogomoletz Str., 01024, Kyiv, Ukraine
| | - Dmitriy Volochnyuk
- Enamine Ltd., 78 Chervonotkatska Str., 02660, Kyiv, Ukraine
- Institute of High Technologies, Taras Shevchenko National University of Kyiv., Glushkova Ave, 03022, Kyiv, Ukraine
- Institute of organic chemistry NAS of Ukraine, 5 Murmanska Str., 02660, Kyiv, Ukraine
| |
Collapse
|
25
|
Flachsenberg F, Ehrt C, Gutermuth T, Rarey M. Redocking the PDB. J Chem Inf Model 2024; 64:219-237. [PMID: 38108627 DOI: 10.1021/acs.jcim.3c01573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Molecular docking is a standard technique in structure-based drug design (SBDD). It aims to predict the 3D structure of a small molecule in the binding site of a receptor (often a protein). Despite being a common technique, it often necessitates multiple tools and involves manual steps. Here, we present the JAMDA preprocessing and docking workflow that is easy to use and allows fully automated docking. We evaluate the JAMDA docking workflow on binding sites extracted from the complete PDB and derive key factors determining JAMDA's docking performance. With that, we try to remove most of the bias due to manual intervention and provide a realistic estimate of the redocking performance of our JAMDA preprocessing and docking workflow for any PDB structure. On this large PDBScan22 data set, our JAMDA workflow finds a pose with an RMSD of at most 2 Å to the crystal ligand on the top rank for 30.1% of the structures. When applying objective structure quality filters to the PDBScan22 data set, the success rate increases to 61.8%. Given the prepared structures from the JAMDA preprocessing pipeline, both JAMDA and the widely used AutoDock Vina perform comparably on this filtered data set (the PDBScan22-HQ data set).
Collapse
Affiliation(s)
- Florian Flachsenberg
- Universität Hamburg, ZBH - Center for Bioinformatics, Bundesstraße 43, 20146 Hamburg, Germany
| | - Christiane Ehrt
- Universität Hamburg, ZBH - Center for Bioinformatics, Bundesstraße 43, 20146 Hamburg, Germany
| | - Torben Gutermuth
- Universität Hamburg, ZBH - Center for Bioinformatics, Bundesstraße 43, 20146 Hamburg, Germany
| | - Matthias Rarey
- Universität Hamburg, ZBH - Center for Bioinformatics, Bundesstraße 43, 20146 Hamburg, Germany
| |
Collapse
|
26
|
Nguyen HT, Van KT, Pham-The H, Braire J, Thi PH, Nguyen TA, Nguyen Thi QG, Dang Thi TA, Le-Nhat-Thuy G, Le Thi TA, Ngoc DV, Nguyen Van T. Synthesis, molecular docking analysis and in vitro evaluation of new heterocyclic hybrids of 4-aza-podophyllotoxin as potent cytotoxic agents. RSC Adv 2024; 14:1838-1853. [PMID: 38192320 PMCID: PMC10772362 DOI: 10.1039/d3ra07396c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 12/27/2023] [Indexed: 01/10/2024] Open
Abstract
Two different synthetic approaches to novel heterocyclic hybrid compounds of 4-azapodophyllotoxin were investigated. The obtained products were characterized by infrared spectroscopy, nuclear magnetic resonance spectroscopy, and high-resolution mass spectrometry. MTT protocol was then performed to examine the cytotoxic activity of these products against KB, HepG2, A549, MCF7, and Hek-293 cell lines. The cytotoxic assessment indicated that all products displayed moderate to high cytotoxicity against all tested cancer cell lines. The most active compound 13k containing the 2-methoxypyridin-4-yl group exhibited selective cytotoxicity against KB, A549, and HepG2 cell lines with the IC50 values ranging from 0.23 to 0.27 μM, which were between 5- to 10-fold more potent than the positive control ellipticine. Compounds 13a (HetAr = thiophen-3-yl) and 13d (HetAr = 5-bromofuran-2-yl) displayed high cytotoxic selectivity for A549 and HepG2 cancer cell lines when compared to the other cancer cell lines and low toxicity to the normal Hek-293 cell line. Molecular docking study was conducted to evaluate the interaction of new synthesized compounds with the colchicine-binding-site of tubulin. Besides that, physicochemical and pharmacokinetic properties of the most active compounds 13h,k were predicted.
Collapse
Affiliation(s)
- Ha Thanh Nguyen
- Institute of Chemistry, Vietnam Academy of Science and Technology 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
| | - Ket Tran Van
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
- Military Technical Academy 236 Hoang Quoc Viet, Bac Tu Liem Hanoi Vietnam
| | - Hai Pham-The
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
| | - Julien Braire
- Université de Rennes 1 2 Av. du Professeur Léon Bernard 35042 Rennes France
| | - Phuong Hoang Thi
- Institute of Chemistry, Vietnam Academy of Science and Technology 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
| | - Tuan Anh Nguyen
- Institute of Chemistry, Vietnam Academy of Science and Technology 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
| | - Quynh Giang Nguyen Thi
- Institute of Chemistry, Vietnam Academy of Science and Technology 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
| | - Tuyet Anh Dang Thi
- Institute of Chemistry, Vietnam Academy of Science and Technology 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
| | - Giang Le-Nhat-Thuy
- Institute of Chemistry, Vietnam Academy of Science and Technology 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
| | - Tu Anh Le Thi
- Institute of Chemistry, Vietnam Academy of Science and Technology 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
| | - Doan Vu Ngoc
- Military Technical Academy 236 Hoang Quoc Viet, Bac Tu Liem Hanoi Vietnam
| | - Tuyen Nguyen Van
- Institute of Chemistry, Vietnam Academy of Science and Technology 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
| |
Collapse
|
27
|
Jarończyk M, Abagyan R, Totrov M. Software and Databases for Protein-Protein Docking. Methods Mol Biol 2024; 2780:129-138. [PMID: 38987467 DOI: 10.1007/978-1-0716-3985-6_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
Protein-protein interactions (PPIs) provide valuable insights for understanding the principles of biological systems and for elucidating causes of incurable diseases. One of the techniques used for computational prediction of PPIs is protein-protein docking calculations, and a variety of software has been developed. This chapter is a summary of software and databases used for protein-protein docking.
Collapse
Affiliation(s)
| | - Ruben Abagyan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | | |
Collapse
|
28
|
Ghith A, Bell SG. The oxidation of steroid derivatives by the CYP125A6 and CYP125A7 enzymes from Mycobacterium marinum. J Steroid Biochem Mol Biol 2023; 235:106406. [PMID: 37793577 DOI: 10.1016/j.jsbmb.2023.106406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/24/2023] [Accepted: 09/30/2023] [Indexed: 10/06/2023]
Abstract
The members of the bacterial cytochrome P450 (CYP) monooxygenase family CYP125, catalyze the oxidation of steroid derivatives including cholesterol and phytosterols, as the initial activating step in their catabolism. However, several bacterial species contain multiple genes encoding CYP125 enzymes and other CYP enzymes which catalyze cholesterol/cholest-4-en-3-one hydroxylation. An important question is why these bacterium have more than one enzyme with overlapping substrate ranges capable of catalyzing the terminal oxidation of the alkyl chain of these sterols. To further understand the role of these enzymes we investigated CYP125A6 and CYP125A7 from Mycobacterium marinum with various cholesterol analogues. These have modifications on the A and B rings of the steroid and we assessed the substrate binding and catalytic activity of these with each enzyme. CYP125A7 gave similar results to those reported for the CYP125A1 enzyme from M. tuberculosis. Differences in the substrate binding and catalytic activity with the cholesterol analogues were observed with CYP125A6. For example, while cholesteryl sulfate could bind to both enzymes it was only oxidized by CYP125A6 and not by CYP125A7. CYP125A6 generated higher levels of metabolites with the majority of C-3 and C-7 substituted cholesterol analogues such 7-ketocholesterol. However, 5α-cholestan-3β-ol was only oxidized by CYP125A7 enzyme. The cholest-4-en-3-one and 7-ketocholesterol-bound forms of the CYP125A6 and CYP125A7 enzymes were modelled using AlphaFold. The structural models highlighted differences in the binding modes of the steroid derivatives within the same enzyme. Significant changes in the binding mode of the steroids between these CYP125 enzymes and other bacterial cholesterol oxidizing enzymes, CYP142A3 and CYP124A1, were also seen. Despite this, all these models predicted the selectivity for terminal methyl hydroxylation, in agreement with the experimental data.
Collapse
Affiliation(s)
- Amna Ghith
- Department of Chemistry, University of Adelaide, SA 5005, Australia
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide, SA 5005, Australia.
| |
Collapse
|
29
|
Palasis KA, Peddie V, Turner DJL, Zhang X, Yu J, Abell AD. Exploring Photoswitchable Binding Interactions with Small-Molecule- and Peptide-Based Inhibitors of Trypsin. Chembiochem 2023; 24:e202300453. [PMID: 37584529 DOI: 10.1002/cbic.202300453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 08/13/2023] [Accepted: 08/14/2023] [Indexed: 08/17/2023]
Abstract
The ability to photochemically activate a drug, both when and where needed, requires optimisation of the difference in biological activity between each isomeric state. As a step to this goal, we report small-molecule- and peptide-based inhibitors of the same protease-trypsin-to better understand how photoswitchable drugs interact with their biological target. The best peptidic inhibitor displayed a more than fivefold difference in inhibitory activity between isomeric states, whereas the best small-molecule inhibitor only showed a 3.4-fold difference. Docking and molecular modelling suggest this result is due to a large change in 3D structure in the key binding residues of the peptidic inhibitor upon isomerisation; this is not observed for the small-molecule inhibitor. Hence, we demonstrate that significant structural changes in critical binding motifs upon irradiation are essential for maximising the difference in biological activity between isomeric states. This is an important consideration in the design of future photoswitchable drugs for clinical applications.
Collapse
Affiliation(s)
- Kathryn A Palasis
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Institute for Photonics and Advanced Sensing (IPAS), Department of Chemistry, The University of Adelaide, North Terrace, Adelaide, SA 5005, Australia
| | - Victoria Peddie
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Institute for Photonics and Advanced Sensing (IPAS), Department of Chemistry, The University of Adelaide, North Terrace, Adelaide, SA 5005, Australia
| | - Dion J L Turner
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Institute for Photonics and Advanced Sensing (IPAS), Department of Chemistry, The University of Adelaide, North Terrace, Adelaide, SA 5005, Australia
| | - Xiaozhou Zhang
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Institute for Photonics and Advanced Sensing (IPAS), Department of Chemistry, The University of Adelaide, North Terrace, Adelaide, SA 5005, Australia
| | - Jingxian Yu
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Institute for Photonics and Advanced Sensing (IPAS), Department of Chemistry, The University of Adelaide, North Terrace, Adelaide, SA 5005, Australia
- Guangxi Key Laboratory of Electrochemical and, Magneto-chemical Functional Materials, College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, 541004, P. R. China
| | - Andrew D Abell
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Institute for Photonics and Advanced Sensing (IPAS), Department of Chemistry, The University of Adelaide, North Terrace, Adelaide, SA 5005, Australia
| |
Collapse
|
30
|
Chan M, Sahakyan H, Eldstrom J, Sastre D, Wang Y, Dou Y, Pourrier M, Vardanyan V, Fedida D. A generic binding pocket for small molecule IKs activators at the extracellular inter-subunit interface of KCNQ1 and KCNE1 channel complexes. eLife 2023; 12:RP87038. [PMID: 37707495 PMCID: PMC10501768 DOI: 10.7554/elife.87038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2023] Open
Abstract
The cardiac IKs ion channel comprises KCNQ1, calmodulin, and KCNE1 in a dodecameric complex which provides a repolarizing current reserve at higher heart rates and protects from arrhythmia syndromes that cause fainting and sudden death. Pharmacological activators of IKs are therefore of interest both scientifically and therapeutically for treatment of IKs loss-of-function disorders. One group of chemical activators are only active in the presence of the accessory KCNE1 subunit and here we investigate this phenomenon using molecular modeling techniques and mutagenesis scanning in mammalian cells. A generalized activator binding pocket is formed extracellularly by KCNE1, the domain-swapped S1 helices of one KCNQ1 subunit and the pore/turret region made up of two other KCNQ1 subunits. A few residues, including K41, A44 and Y46 in KCNE1, W323 in the KCNQ1 pore, and Y148 in the KCNQ1 S1 domain, appear critical for the binding of structurally diverse molecules, but in addition, molecular modeling studies suggest that induced fit by structurally different molecules underlies the generalized nature of the binding pocket. Activation of IKs is enhanced by stabilization of the KCNQ1-S1/KCNE1/pore complex, which ultimately slows deactivation of the current, and promotes outward current summation at higher pulse rates. Our results provide a mechanistic explanation of enhanced IKs currents by these activator compounds and provide a map for future design of more potent therapeutically useful molecules.
Collapse
Affiliation(s)
- Magnus Chan
- Department of Anesthesiology, Pharmacology and Therapeutics, University of British ColumbiaVancouverCanada
| | - Harutyun Sahakyan
- Laboratory of Computational Modeling of Biological Processes, Institute of Molecular BiologyYerevanArmenia
| | - Jodene Eldstrom
- Department of Anesthesiology, Pharmacology and Therapeutics, University of British ColumbiaVancouverCanada
| | - Daniel Sastre
- Department of Anesthesiology, Pharmacology and Therapeutics, University of British ColumbiaVancouverCanada
| | - Yundi Wang
- Department of Anesthesiology, Pharmacology and Therapeutics, University of British ColumbiaVancouverCanada
| | - Ying Dou
- Department of Anesthesiology, Pharmacology and Therapeutics, University of British ColumbiaVancouverCanada
| | - Marc Pourrier
- Department of Anesthesiology, Pharmacology and Therapeutics, University of British ColumbiaVancouverCanada
| | - Vitya Vardanyan
- Molecular Neuroscience Group, Institute of Molecular BiologyYerevanArmenia
| | - David Fedida
- Department of Anesthesiology, Pharmacology and Therapeutics, University of British ColumbiaVancouverCanada
| |
Collapse
|
31
|
Abdelrahman KS, Hassan HA, Abdel-Aziz SA, Marzouk AA, Shams R, Osawa K, Abdel-Aziz M, Konno H. Development and Assessment of 1,5-Diarylpyrazole/Oxime Hybrids Targeting EGFR and JNK-2 as Antiproliferative Agents: A Comprehensive Study through Synthesis, Molecular Docking, and Evaluation. Molecules 2023; 28:6521. [PMID: 37764297 PMCID: PMC10537604 DOI: 10.3390/molecules28186521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
New 1,5-diarylpyrazole oxime hybrid derivatives (scaffolds A and B) were designed, synthesized, and then their purity was verified using a variety of spectroscopic methods. A panel of five cancer cell lines known to express EGFR and JNK-2, including human colorectal adenocarcinoma cell line DLD-1, human cervical cancer cell line Hela, human leukemia cell line K562, human pancreatic cell line SUIT-2, and human hepatocellular carcinoma cell line HepG2, were used to biologically evaluate for their in vitro cytotoxicity for all the synthesized compounds 7a-j, 8a-j, 9a-c, and 10a-c. The oxime containing compounds 8a-j and 10a-c were more active as antiproliferative agents than their non-oxime congeners 7a-j and 9a-c. Compounds 8d, 8g, 8i, and 10c inhibited EGFR with IC50 values ranging from 8 to 21 µM when compared with sorafenib. Compound 8i inhibited JNK-2 as effectively as sorafenib, with an IC50 of 1.0 µM. Furthermore, compound 8g showed cell cycle arrest at the G2/M phase in the cell cycle analysis of the Hela cell line, whereas compound 8i showed combined S phase and G2 phase arrest. According to docking studies, oxime hybrid compounds 8d, 8g, 8i, and 10c exhibited binding free energies ranging from -12.98 to 32.30 kcal/mol at the EGFR binding site whereas compounds 8d and 8i had binding free energies ranging from -9.16 to -12.00 kcal/mol at the JNK-2 binding site.
Collapse
Affiliation(s)
- Kamal S. Abdelrahman
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Al-Azhar University, Assiut Branch, Assiut 71524, Egypt; (S.A.A.-A.); (A.A.M.)
| | - Heba A. Hassan
- Department of Medicinal Chemistry Faculty of Pharmacy, Minia University, Minia 61519, Egypt; (H.A.H.); (M.A.-A.)
| | - Salah A. Abdel-Aziz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Al-Azhar University, Assiut Branch, Assiut 71524, Egypt; (S.A.A.-A.); (A.A.M.)
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Deraya University, Minia 61768, Egypt
| | - Adel A. Marzouk
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Al-Azhar University, Assiut Branch, Assiut 71524, Egypt; (S.A.A.-A.); (A.A.M.)
- National Center for Natural Products Research, School of Pharmacy, University of Missippi, Oxford, MS 38677, USA
| | - Raef Shams
- Emergent Bioengineering Materials Research Team, RIKEN Centre for Emergent Matter Science, RIKEN, Wako 351-0198, Saitama, Japan;
| | - Keima Osawa
- Graduate School of Science and Engineering, Yamagata University, Yonezawa 992-8510, Yamagata, Japan;
| | - Mohamed Abdel-Aziz
- Department of Medicinal Chemistry Faculty of Pharmacy, Minia University, Minia 61519, Egypt; (H.A.H.); (M.A.-A.)
| | - Hiroyuki Konno
- Graduate School of Science and Engineering, Yamagata University, Yonezawa 992-8510, Yamagata, Japan;
| |
Collapse
|
32
|
Bendary MM, Abd El-Hamid MI, Abousaty AI, Elmanakhly AR, Alshareef WA, Mosbah RA, Alhomrani M, Ghoneim MM, Elkelish A, Hashim N, Alamri AS, Al-Harthi HF, Safwat NA. Therapeutic Switching of Rafoxanide: a New Approach To Fighting Drug-Resistant Bacteria and Fungi. Microbiol Spectr 2023; 11:e0267922. [PMID: 37458598 PMCID: PMC10433953 DOI: 10.1128/spectrum.02679-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 06/05/2023] [Indexed: 08/19/2023] Open
Abstract
Control and management of life-threatening bacterial and fungal infections are a global health challenge. Despite advances in antimicrobial therapies, treatment failures for resistant bacterial and fungal infections continue to increase. We aimed to repurpose the anthelmintic drug rafoxanide for use with existing therapeutic drugs to increase the possibility of better managing infection and decrease treatment failures. For this purpose, we evaluated the antibacterial and antifungal potential of rafoxanide. Notably, 70% (70/100) of bacterial isolates showed multidrug resistance (MDR) patterns, with higher prevalence among human isolates (73.5% [50/68]) than animal ones (62.5% [20/32]). Moreover, 22 fungal isolates (88%) were MDR and were more prevalent among animal (88.9%) than human (87.5%) sources. We observed alarming MDR patterns among bacterial isolates, i.e., Klebsiella pneumoniae (75% [30/40; 8 animal and 22 human]) and Escherichia coli (66% [40/60; 12 animal and 28 human]), and fungal isolates, i.e., Candida albicans (86.7% [13/15; 4 animal and 9 human]) and Aspergillus fumigatus (90% [9/10; 4 animal and 5 human]), that were resistant to at least one agent in three or more different antimicrobial classes. Rafoxanide had antibacterial and antifungal activities, with minimal inhibitory concentration (MICs) ranging from 2 to 128 μg/mL. Rafoxanide at sub-MICs downregulated the mRNA expression of resistance genes, including E. coli and K. pneumoniae blaCTX-M-1, blaTEM-1, blaSHV, MOX, and DHA, C. albicans ERG11, and A. fumigatus cyp51A. We noted the improvement in the activity of β-lactam and antifungal drugs upon combination with rafoxanide. This was apparent in the reduction in the MICs of cefotaxime and fluconazole when these drugs were combined with sub-MIC levels of rafoxanide. There was obvious synergism between rafoxanide and cefotaxime against all E. coli and K. pneumoniae isolates (fractional inhibitory concentration index [FICI] values ≤ 0.5). Accordingly, there was a shift in the patterns of resistance of 16.7% of E. coli and 22.5% of K. pneumoniae isolates to cefotaxime and those of 63.2% of C. albicans and A. fumigatus isolates to fluconazole when the isolates were treated with sub-MICs of rafoxanide. These results were confirmed by in silico and mouse protection assays. Based on the in silico study, one possible explanation for how rafoxanide reduced bacterial resistance is through its inhibitory effects on bacterial and fungal histidine kinase enzymes. In short, rafoxanide exhibited promising results in overcoming bacterial and fungal drug resistance. IMPORTANCE The drug repurposing strategy is an alternative approach to reducing drug development timelines with low cost, especially during outbreaks of disease caused by drug-resistant pathogens. Rafoxanide can disrupt the abilities of bacterial and fungal cells to adapt to stress conditions. The coadministration of antibiotics with rafoxanide can prevent the failure of treatment of both resistant bacteria and fungi, as the resistant pathogens could be made sensitive upon treatment with rafoxanide. From our findings, we anticipate that pharmaceutical companies will be able to utilize new combinations against resistant pathogens.
Collapse
Affiliation(s)
- Mahmoud M. Bendary
- Department of Microbiology and Immunology, Faculty of Pharmacy, Port Said University, Port Said, Egypt
| | - Marwa I. Abd El-Hamid
- Department of Microbiology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Amira I. Abousaty
- Department of Microbiology, Faculty of Science, Zagazig University, Zagazig, Egypt
| | - Arwa R. Elmanakhly
- Department of Microbiology and Immunology, Faculty of Pharmacy, Modern University for Technology and Information, Cairo, Egypt
| | - Walaa A. Alshareef
- Department of Microbiology and Immunology, Faculty of Pharmacy, October 6 University, 6th of October, Egypt
| | - Rasha A. Mosbah
- Infection Control Unit, Zagazig University Hospital, Zagazig, Egypt
| | - Majid Alhomrani
- Department of Clinical Laboratories Sciences, The Faculty of Applied Medical Science, Taif University, Taif, Saudi Arabia
- Centre of Biomedical Science Research, Deanship of Scientific Research, Taif University, Taif, Saudi Arabia
| | - Mohammed M. Ghoneim
- Department of Pharmacy Practice, College of Pharmacy, Al Maarefa University, Ad Diriyah, Saudi Arabia
| | - Amr Elkelish
- Biology Department, College of Science, Imam Mohammad ibn Saud Islamic University, Riyadh, Saudi Arabia
- Botany and Microbiology Department, Faculty of Science, Suez Canal University, Ismailia, Egypt
| | - Nada Hashim
- Faculty of Medicine, University of Gezira, Wad Medani, Sudan
| | - Abdulhakeem S. Alamri
- Department of Clinical Laboratories Sciences, The Faculty of Applied Medical Science, Taif University, Taif, Saudi Arabia
- Centre of Biomedical Science Research, Deanship of Scientific Research, Taif University, Taif, Saudi Arabia
| | - Helal F. Al-Harthi
- Biology Department, Turabah University College, Taif University, Taif, Saudi Arabia
| | - Nesreen A. Safwat
- Department of Microbiology and Immunology, Faculty of Pharmacy, Modern University for Technology and Information, Cairo, Egypt
| |
Collapse
|
33
|
Shamsara J, Schüürmann G. Improvement of binding pose prediction of the MR1 covalent ligands by inclusion of simple pharmacophore constraints and structural waters in the docking process. 3 Biotech 2023; 13:279. [PMID: 37483466 PMCID: PMC10356737 DOI: 10.1007/s13205-023-03694-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 06/29/2023] [Indexed: 07/25/2023] Open
Abstract
The major histocompatibility complex (MHC) class I-related molecule, MR1, is a key component of the immune system, presenting antigens to T-cell receptors (TCRs) and modulating the immune response against various antigens. MR1 possesses a compact ligand-binding pocket despite its ability to interact with ligands that can have either agonistic or antagonistic effects on the immune system. Agonistic ligands can stimulate the immune response, while antagonistic ligands do not elicit an immune response. In most cases, ligand binding to MR1 is mediated through a covalent bond with Lys43. However, recent studies have suggested that a variety of small molecules can interact with the MR1-binding site. In this study, we have used several approaches to improve the binding pose prediction of covalent ligands to MR1, including docking in mutated receptors, and imposing simple pharmacophore constraints and structural water molecules. The careful assignment of pharmacophore constraints and inclusion of structural water molecules in the challenging docking process of covalent docking improved the binding pose prediction and virtual screening performance. In a retrospective virtual screening, the proposed approach exhibited EF1% and EF2% values of 7.4 and 5.5, respectively. Conversely, when using the mutated receptor, both EF1% and EF2% were recorded as 0 for the conventional docking method. The performance of the pharmacophore constraints was also evaluated on other covalent docking cases, and compared to previously reported results for common covalent docking methods. The proposed approach achieved an average RMSD of 2.55, while AutoDock4, CovDock, FITTED, GOLD, ICM-Pro, and MOE exhibited average RMSD values of 3.0, 2.93, 3.04, 4.93, 2.44, and 3.36, respectively. Our results demonstrate that the inclusion of simple pharmacophore constraints and structural waters can improve the prediction of binding poses of covalent ligands to MR1, which can aid in the discovery of novel immunotherapeutic agents. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03694-w.
Collapse
Affiliation(s)
- Jamal Shamsara
- UFZ Department of Ecological Chemistry, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Gerrit Schüürmann
- UFZ Department of Ecological Chemistry, Helmholtz Centre for Environmental Research, Leipzig, Germany
- Institute of Organic Chemistry, Technical University Bergakademie Freiberg, Freiberg, Germany
| |
Collapse
|
34
|
Clayton-Cuch D, McDougal D, Schwerdt JG, Yu L, Shirley N, Bradley D, Bruning JB, Böttcher C, Bulone V. Identification and characterisation of MdUGT78T2 as a galactosyltransferase with dual activity on flavonol and anthocyanidin substrates in red-skinned apple fruit (Malus domestica L.). Food Chem 2023; 424:136388. [PMID: 37220682 DOI: 10.1016/j.foodchem.2023.136388] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 04/20/2023] [Accepted: 05/13/2023] [Indexed: 05/25/2023]
Abstract
Anthocyanidin and flavonol glycosides have been linked to the health-promoting effects associated with apple consumption. However, very few enzymes involved in flavonoid glycosylation have been characterised to date. Here, we present the identification and phylogenetic analysis of 234 putative glycosyltransferases involved in flavonoid biosynthesis, and detail the biochemical and structural characterisation of MdUGT78T2 as a strict galactosyltransferase involved in the formation of quercetin-3-O-galactoside and cyanidin-3-O-galactoside, the major glycoconjugates of flavonoids in apple. The enzyme is also active on other flavonoids but with a lower catalytic efficiency. Our data, complemented with gene expression analysis suggest that MdUGT78T2 synthesises the glycoconjugates at both the early and late stages of fruit development. This newly discovered type of catalytic activity can potentially be exploited for in vitro modification of flavonoids to increase their stability in food products and to modify apple fruits and other commercial crops through breeding approaches to enhance their health benefits.
Collapse
Affiliation(s)
- Daniel Clayton-Cuch
- Adelaide Glycomics, The University of Adelaide, School of Agriculture, Food and Wine, Waite Campus, Adelaide, South Australia 5064, Australia; CSIRO, Waite Campus, Glen Osmond, South Australia 5064, Australia
| | - Daniel McDougal
- Institute for Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Julian G Schwerdt
- Adelaide Glycomics, The University of Adelaide, School of Agriculture, Food and Wine, Waite Campus, Adelaide, South Australia 5064, Australia
| | - Long Yu
- Adelaide Glycomics, The University of Adelaide, School of Agriculture, Food and Wine, Waite Campus, Adelaide, South Australia 5064, Australia
| | - Neil Shirley
- Adelaide Glycomics, The University of Adelaide, School of Agriculture, Food and Wine, Waite Campus, Adelaide, South Australia 5064, Australia
| | - David Bradley
- Agilent Technologies Australia Pty Ltd, Mulgrave, Melbourne, Victoria, Australia
| | - John B Bruning
- Institute for Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | | | - Vincent Bulone
- Adelaide Glycomics, The University of Adelaide, School of Agriculture, Food and Wine, Waite Campus, Adelaide, South Australia 5064, Australia; Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm, Sweden.
| |
Collapse
|
35
|
Meewan I, Shiryaev SA, Kattoula J, Huang CT, Lin V, Chuang CH, Terskikh AV, Abagyan R. Allosteric Inhibitors of Zika Virus NS2B-NS3 Protease Targeting Protease in "Super-Open" Conformation. Viruses 2023; 15:v15051106. [PMID: 37243192 DOI: 10.3390/v15051106] [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: 02/21/2023] [Revised: 04/26/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023] Open
Abstract
The Zika virus (ZIKV), a member of the Flaviviridae family, is considered a major health threat causing multiple cases of microcephaly in newborns and Guillain-Barré syndrome in adults. In this study, we targeted a transient, deep, and hydrophobic pocket of the "super-open" conformation of ZIKV NS2B-NS3 protease to overcome the limitations of the active site pocket. After virtual docking screening of approximately seven million compounds against the novel allosteric site, we selected the top six candidates and assessed them in enzymatic assays. Six candidates inhibited ZIKV NS2B-NS3 protease proteolytic activity at low micromolar concentrations. These six compounds, targeting the selected protease pocket conserved in ZIKV, serve as unique drug candidates and open new opportunities for possible treatment against several flavivirus infections.
Collapse
Affiliation(s)
- Ittipat Meewan
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom 73170, Thailand
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Sergey A Shiryaev
- Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Julius Kattoula
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Chun-Teng Huang
- Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Vivian Lin
- Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Chiao-Han Chuang
- Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Alexey V Terskikh
- Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Ruben Abagyan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
| |
Collapse
|
36
|
Bao LQ, Baecker D, Mai Dung DT, Phuong Nhung N, Thi Thuan N, Nguyen PL, Phuong Dung PT, Huong TTL, Rasulev B, Casanola-Martin GM, Nam NH, Pham-The H. Development of Activity Rules and Chemical Fragment Design for In Silico Discovery of AChE and BACE1 Dual Inhibitors against Alzheimer's Disease. Molecules 2023; 28:molecules28083588. [PMID: 37110831 PMCID: PMC10142303 DOI: 10.3390/molecules28083588] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/15/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
Multi-target drug development has become an attractive strategy in the discovery of drugs to treat of Alzheimer's disease (AzD). In this study, for the first time, a rule-based machine learning (ML) approach with classification trees (CT) was applied for the rational design of novel dual-target acetylcholinesterase (AChE) and β-site amyloid-protein precursor cleaving enzyme 1 (BACE1) inhibitors. Updated data from 3524 compounds with AChE and BACE1 measurements were curated from the ChEMBL database. The best global accuracies of training/external validation for AChE and BACE1 were 0.85/0.80 and 0.83/0.81, respectively. The rules were then applied to screen dual inhibitors from the original databases. Based on the best rules obtained from each classification tree, a set of potential AChE and BACE1 inhibitors were identified, and active fragments were extracted using Murcko-type decomposition analysis. More than 250 novel inhibitors were designed in silico based on active fragments and predicted AChE and BACE1 inhibitory activity using consensus QSAR models and docking validations. The rule-based and ML approach applied in this study may be useful for the in silico design and screening of new AChE and BACE1 dual inhibitors against AzD.
Collapse
Affiliation(s)
- Le-Quang Bao
- Department of Pharmaceutical Chemistry, Hanoi University of Pharmacy, 13-15 Le Thanh Tong, Hoan Kiem, Hanoi 10000, Vietnam
| | - Daniel Baecker
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, University of Greifswald, Friedrich-Ludwig-Jahn-Straße 17, 17489 Greifswald, Germany
| | - Do Thi Mai Dung
- Department of Pharmaceutical Chemistry, Hanoi University of Pharmacy, 13-15 Le Thanh Tong, Hoan Kiem, Hanoi 10000, Vietnam
| | - Nguyen Phuong Nhung
- Department of Pharmaceutical Chemistry, Hanoi University of Pharmacy, 13-15 Le Thanh Tong, Hoan Kiem, Hanoi 10000, Vietnam
| | - Nguyen Thi Thuan
- Department of Pharmaceutical Chemistry, Hanoi University of Pharmacy, 13-15 Le Thanh Tong, Hoan Kiem, Hanoi 10000, Vietnam
| | - Phuong Linh Nguyen
- College of Computing & Informatics, Drexel University, 3141 Chestnut St., Philadelphia, PA 19104, USA
| | - Phan Thi Phuong Dung
- Department of Pharmaceutical Chemistry, Hanoi University of Pharmacy, 13-15 Le Thanh Tong, Hoan Kiem, Hanoi 10000, Vietnam
| | - Tran Thi Lan Huong
- Department of Pharmaceutical Chemistry, Hanoi University of Pharmacy, 13-15 Le Thanh Tong, Hoan Kiem, Hanoi 10000, Vietnam
| | - Bakhtiyor Rasulev
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, ND 58102, USA
| | | | - Nguyen-Hai Nam
- Department of Pharmaceutical Chemistry, Hanoi University of Pharmacy, 13-15 Le Thanh Tong, Hoan Kiem, Hanoi 10000, Vietnam
| | - Hai Pham-The
- Department of Pharmaceutical Chemistry, Hanoi University of Pharmacy, 13-15 Le Thanh Tong, Hoan Kiem, Hanoi 10000, Vietnam
| |
Collapse
|
37
|
Bagnolini G, Luu TB, Hargrove AE. Recognizing the power of machine learning and other computational methods to accelerate progress in small molecule targeting of RNA. RNA (NEW YORK, N.Y.) 2023; 29:473-488. [PMID: 36693763 PMCID: PMC10019373 DOI: 10.1261/rna.079497.122] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
RNA structures regulate a wide range of processes in biology and disease, yet small molecule chemical probes or drugs that can modulate these functions are rare. Machine learning and other computational methods are well poised to fill gaps in knowledge and overcome the inherent challenges in RNA targeting, such as the dynamic nature of RNA and the difficulty of obtaining RNA high-resolution structures. Successful tools to date include principal component analysis, linear discriminate analysis, k-nearest neighbor, artificial neural networks, multiple linear regression, and many others. Employment of these tools has revealed critical factors for selective recognition in RNA:small molecule complexes, predictable differences in RNA- and protein-binding ligands, and quantitative structure activity relationships that allow the rational design of small molecules for a given RNA target. Herein we present our perspective on the value of using machine learning and other computation methods to advance RNA:small molecule targeting, including select examples and their validation as well as necessary and promising future directions that will be key to accelerate discoveries in this important field.
Collapse
Affiliation(s)
- Greta Bagnolini
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - TinTin B Luu
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - Amanda E Hargrove
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, USA
| |
Collapse
|
38
|
Sadybekov AV, Katritch V. Computational approaches streamlining drug discovery. Nature 2023; 616:673-685. [PMID: 37100941 DOI: 10.1038/s41586-023-05905-z] [Citation(s) in RCA: 300] [Impact Index Per Article: 150.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 03/01/2023] [Indexed: 04/28/2023]
Abstract
Computer-aided drug discovery has been around for decades, although the past few years have seen a tectonic shift towards embracing computational technologies in both academia and pharma. This shift is largely defined by the flood of data on ligand properties and binding to therapeutic targets and their 3D structures, abundant computing capacities and the advent of on-demand virtual libraries of drug-like small molecules in their billions. Taking full advantage of these resources requires fast computational methods for effective ligand screening. This includes structure-based virtual screening of gigascale chemical spaces, further facilitated by fast iterative screening approaches. Highly synergistic are developments in deep learning predictions of ligand properties and target activities in lieu of receptor structure. Here we review recent advances in ligand discovery technologies, their potential for reshaping the whole process of drug discovery and development, as well as the challenges they encounter. We also discuss how the rapid identification of highly diverse, potent, target-selective and drug-like ligands to protein targets can democratize the drug discovery process, presenting new opportunities for the cost-effective development of safer and more effective small-molecule treatments.
Collapse
Affiliation(s)
- Anastasiia V Sadybekov
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
- Center for New Technologies in Drug Discovery and Development, Bridge Institute, Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA
| | - Vsevolod Katritch
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.
- Center for New Technologies in Drug Discovery and Development, Bridge Institute, Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA.
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA.
| |
Collapse
|
39
|
Zhao S, Zhang X, da Silva-Júnior EF, Zhan P, Liu X. Computer-aided drug design in seeking viral capsid modulators. Drug Discov Today 2023; 28:103581. [PMID: 37030533 DOI: 10.1016/j.drudis.2023.103581] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/16/2023] [Accepted: 03/30/2023] [Indexed: 04/09/2023]
Abstract
Approved or licensed antiviral drugs have limited applications because of their drug resistance and severe adverse effects. By contrast, by stabilizing or destroying the viral capsid, compounds known as capsid modulators prevent viral replication by acting on new targets and, therefore, overcoming the problem of clinical drug resistance. For example. computer-aided drug design (CADD) methods, using strategies based on structures of biological targets (structure-based drug design; SBDD), such as docking, molecular dynamics (MD) simulations, and virtual screening (VS), have provided opportunities for fast and effective development of viral capsid modulators. In this review, we summarize the application of CADD in the discovery, optimization, and mechanism prediction of capsid-targeting small molecules, providing new insights into antiviral drug discovery modalities. Teaser: Computer-aided drug design will accelerate the development of viral capsid regulators, which brings new hope for the treatment of refractory viral diseases.
Collapse
Affiliation(s)
- Shujie Zhao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Xujie Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Edeildo Ferreira da Silva-Júnior
- Institute of Chemistry and Biotechnology, Federal University of Alagoas, Lourival Melo Mota Avenue, 57072-970 Maceió, Alagoas, Brazil.
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China.
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China.
| |
Collapse
|
40
|
Potlitz F, Link A, Schulig L. Advances in the discovery of new chemotypes through ultra-large library docking. Expert Opin Drug Discov 2023; 18:303-313. [PMID: 36714919 DOI: 10.1080/17460441.2023.2171984] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
INTRODUCTION The size and complexity of virtual screening libraries in drug discovery have skyrocketed in recent years, reaching up to multiple billions of accessible compounds. However, virtual screening of such ultra-large libraries poses several challenges associated with preparing the libraries, sampling, and pre-selection of suitable compounds. The utilization of artificial intelligence (AI)-assisted screening approaches, such as deep learning, poses a promising countermeasure to deal with this rapidly expanding chemical space. For example, various AI-driven methods were recently successfully used to identify novel small molecule inhibitors of the SARS-CoV-2 main protease (Mpro). AREAS COVERED This review focuses on presenting various kinds of virtual screening methods suitable for dealing with ultra-large libraries. Challenges associated with these computational methodologies are discussed, and recent advances are highlighted in the example of the discovery of novel Mpro inhibitors targeting the SARS-CoV-2 virus. EXPERT OPINION With the rapid expansion of the virtual chemical space, the methodologies for docking and screening such quantities of molecules need to keep pace. Employment of AI-driven screening compounds has already been shown to be effective in a range from a few thousand to multiple billion compounds, furthered by de novo generation of drug-like molecules without human interference.
Collapse
Affiliation(s)
- Felix Potlitz
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, University of Greifswald, Germany
| | - Andreas Link
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, University of Greifswald, Germany
| | - Lukas Schulig
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, University of Greifswald, Germany
| |
Collapse
|
41
|
Lessons Learnt from COVID-19: Computational Strategies for Facing Present and Future Pandemics. Int J Mol Sci 2023; 24:ijms24054401. [PMID: 36901832 PMCID: PMC10003049 DOI: 10.3390/ijms24054401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/19/2023] [Accepted: 02/21/2023] [Indexed: 02/25/2023] Open
Abstract
Since its outbreak in December 2019, the COVID-19 pandemic has caused the death of more than 6.5 million people around the world. The high transmissibility of its causative agent, the SARS-CoV-2 virus, coupled with its potentially lethal outcome, provoked a profound global economic and social crisis. The urgency of finding suitable pharmacological tools to tame the pandemic shed light on the ever-increasing importance of computer simulations in rationalizing and speeding up the design of new drugs, further stressing the need for developing quick and reliable methods to identify novel active molecules and characterize their mechanism of action. In the present work, we aim at providing the reader with a general overview of the COVID-19 pandemic, discussing the hallmarks in its management, from the initial attempts at drug repurposing to the commercialization of Paxlovid, the first orally available COVID-19 drug. Furthermore, we analyze and discuss the role of computer-aided drug discovery (CADD) techniques, especially those that fall in the structure-based drug design (SBDD) category, in facing present and future pandemics, by showcasing several successful examples of drug discovery campaigns where commonly used methods such as docking and molecular dynamics have been employed in the rational design of effective therapeutic entities against COVID-19.
Collapse
|
42
|
Kamal IM, Chakrabarti S. MetaDOCK: A Combinatorial Molecular Docking Approach. ACS OMEGA 2023; 8:5850-5860. [PMID: 36816658 PMCID: PMC9933224 DOI: 10.1021/acsomega.2c07619] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 01/11/2023] [Indexed: 06/18/2023]
Abstract
Molecular docking plays a major role in academic and industrial drug screening and discovery processes. Despite the availability of numerous docking software packages, there is a lot of scope for improvement for the docking algorithms in terms of becoming more reliable to replicate the experimental binding results. Here, we propose a combinatorial or consensus docking approach where complementary powers of the existing methods are captured. We created a meta-docking protocol by combining the results of AutoDock4.2, LeDock, and rDOCK programs as these are freely available, easy to use, and suitable for large-scale analysis and produced better performance on benchmarking studies. Rigorous benchmarking analyses were undertaken to evaluate the scoring, posing, and screening capability of our approach. Further, the performance measures were compared against one standard state-of-the-art commercial docking software, GOLD, and one freely available software, PLANTS. Performances of MetaDOCK for scoring, posing, and screening the protein-ligand complexes were found to be quite superior compared to the reference programs. Exhaustive molecular dynamics simulation and molecular mechanics Poisson-Boltzmann and surface area-based free energy estimation also suggest better energetic stability of the docking solutions produced by our meta-approach. We believe that the MetaDOCK approach is a useful packaging of the freely available software and provides a better alternative to the scientific community who are unable to afford costly commercial packages.
Collapse
Affiliation(s)
- Izaz Monir Kamal
- Division
of Structural Biology & Bioinformatics, CSIR-Indian Institute of Chemical Biology, Salt Lake, Sector V, Kolkata 700032, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Saikat Chakrabarti
- Division
of Structural Biology & Bioinformatics, CSIR-Indian Institute of Chemical Biology, Salt Lake, Sector V, Kolkata 700032, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| |
Collapse
|
43
|
den Hollander LS, Béquignon OJM, Wang X, van Wezel K, Broekhuis J, Gorostiola González M, de Visser KE, IJzerman AP, van Westen GJP, Heitman LH. Impact of cancer-associated mutations in CC chemokine receptor 2 on receptor function and antagonism. Biochem Pharmacol 2023; 208:115399. [PMID: 36581051 DOI: 10.1016/j.bcp.2022.115399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 12/27/2022]
Abstract
CC chemokine receptor 2 (CCR2), a G protein-coupled receptor, plays a role in many cancer-related processes such as metastasis formation and immunosuppression. Since ∼ 20 % of human cancers contain mutations in G protein-coupled receptors, ten cancer-associated CCR2 mutants obtained from the Genome Data Commons were investigated for their effect on receptor functionality and antagonist binding. Mutations were selected based on either their vicinity to CCR2's orthosteric or allosteric binding sites or their presence in conserved amino acid motifs. One of the mutant receptors, namely S101P2.63 with a mutation near the orthosteric binding site, did not express on the cell surface. All other studied mutants showed a decrease in or a lack of G protein activation in response to the main endogenous CCR2 ligand CCL2, but no change in potency was observed. Furthermore, INCB3344 and LUF7482 were chosen as representative orthosteric and allosteric antagonists, respectively. No change in potency was observed in a functional assay, but mutations located at F1163.28 impacted orthosteric antagonist binding significantly, while allosteric antagonist binding was abolished for L134Q3.46 and D137N3.49 mutants. As CC chemokine receptor 2 is an attractive drug target in cancer, the negative effect of these mutations on receptor functionality and drugability should be considered in the drug discovery process.
Collapse
Affiliation(s)
- L S den Hollander
- Leiden Academic Centre for Drug Research, Division of Drug Discovery and Safety, Leiden, The Netherlands
| | - O J M Béquignon
- Leiden Academic Centre for Drug Research, Division of Drug Discovery and Safety, Leiden, The Netherlands
| | - X Wang
- Leiden Academic Centre for Drug Research, Division of Drug Discovery and Safety, Leiden, The Netherlands
| | - K van Wezel
- Leiden Academic Centre for Drug Research, Division of Drug Discovery and Safety, Leiden, The Netherlands
| | - J Broekhuis
- Leiden Academic Centre for Drug Research, Division of Drug Discovery and Safety, Leiden, The Netherlands
| | - M Gorostiola González
- Leiden Academic Centre for Drug Research, Division of Drug Discovery and Safety, Leiden, The Netherlands; Oncode Institute, Leiden, The Netherlands
| | - K E de Visser
- Oncode Institute, Leiden, The Netherlands; Netherlands Cancer Institute, Division of Tumor Biology & Immunology, Amsterdam, The Netherlands; Leiden University, Department of Immunology, Medical Centre, Leiden, The Netherlands
| | - A P IJzerman
- Leiden Academic Centre for Drug Research, Division of Drug Discovery and Safety, Leiden, The Netherlands
| | - G J P van Westen
- Leiden Academic Centre for Drug Research, Division of Drug Discovery and Safety, Leiden, The Netherlands
| | - L H Heitman
- Leiden Academic Centre for Drug Research, Division of Drug Discovery and Safety, Leiden, The Netherlands; Oncode Institute, Leiden, The Netherlands.
| |
Collapse
|
44
|
Shin J, Mir H, Khurram MA, Fujihara KM, Dynlacht BD, Cardozo TJ, Possemato R. Allosteric regulation of CAD modulates de novo pyrimidine synthesis during the cell cycle. Nat Metab 2023; 5:277-293. [PMID: 36747088 PMCID: PMC10064490 DOI: 10.1038/s42255-023-00735-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 01/03/2023] [Indexed: 02/08/2023]
Abstract
Metabolism is a fundamental cellular process that is coordinated with cell cycle progression. Despite this association, a mechanistic understanding of cell cycle phase-dependent metabolic pathway regulation remains elusive. Here we report the mechanism by which human de novo pyrimidine biosynthesis is allosterically regulated during the cell cycle. Combining traditional synchronization methods and metabolomics, we characterize metabolites by their accumulation pattern during cell cycle phases and identify cell cycle phase-dependent regulation of carbamoyl-phosphate synthetase 2, aspartate transcarbamylase and dihydroorotase (CAD), the first, rate-limiting enzyme in de novo pyrimidine biosynthesis. Through systematic mutational scanning and structural modelling, we find allostery as a major regulatory mechanism that controls the activity change of CAD during the cell cycle. Specifically, we report evidence of two Animalia-specific loops in the CAD allosteric domain that involve sensing and binding of uridine 5'-triphosphate, a CAD allosteric inhibitor. Based on homology with a mitochondrial carbamoyl-phosphate synthetase homologue, we identify a critical role for a signal transmission loop in regulating the formation of a substrate channel, thereby controlling CAD activity.
Collapse
Affiliation(s)
- Jong Shin
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York, NY, USA
| | - Hannan Mir
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York, NY, USA
| | - Maaz A Khurram
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York, NY, USA
| | - Kenji M Fujihara
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York, NY, USA
| | - Brian D Dynlacht
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York, NY, USA
| | - Timothy J Cardozo
- Laura & Isaac Perlmutter Cancer Center, New York, NY, USA
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Richard Possemato
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA.
- Laura & Isaac Perlmutter Cancer Center, New York, NY, USA.
| |
Collapse
|
45
|
Baldassarri C, Giorgioni G, Piergentili A, Quaglia W, Fontana S, Mammoli V, Minazzato G, Marangoni E, Gasparrini M, Sorci L, Raffaelli N, Cappellacci L, Petrelli R, Del Bello F. Properly Substituted Benzimidazoles as a New Promising Class of Nicotinate Phosphoribosyltransferase (NAPRT) Modulators. Pharmaceuticals (Basel) 2023; 16:189. [PMID: 37259338 PMCID: PMC9967085 DOI: 10.3390/ph16020189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/21/2023] [Accepted: 01/24/2023] [Indexed: 09/10/2024] Open
Abstract
The prevention of nicotinamide adenine dinucleotide (NAD) biosynthesis is considered an attractive therapeutic approach against cancer, considering that tumor cells are characterized by an increased need for NAD to fuel their reprogrammed metabolism. On the other hand, the decline of NAD is a hallmark of some pathological conditions, including neurodegeneration and metabolic diseases, and boosting NAD biosynthesis has proven to be of therapeutic relevance. Therefore, targeting the enzymes nicotinamide phosphoribosyltransferase (NAMPT) and nicotinate phosphoribosyltransferase (NAPRT), which regulate NAD biosynthesis from nicotinamide (NAM) and nicotinic acid (NA), respectively, is considered a promising strategy to modulate intracellular NAD pool. While potent NAMPT inhibitors and activators have been developed, the search for NAPRT modulators is still in its infancy. In this work, we report on the identification of a new class of NAPRT modulators bearing the 1,2-dimethylbenzimidazole scaffold properly substituted in position 5. In particular, compounds 24, 31, and 32 emerged as the first NAPRT activators reported so far, while 18 behaved as a noncompetitive inhibitor toward NA (Ki = 338 µM) and a mixed inhibitor toward phosphoribosyl pyrophosphate (PRPP) (Ki = 134 µM). From in vitro pharmacokinetic studies, compound 18 showed an overall good ADME profile. To rationalize the obtained results, docking studies were performed on the NAPRT structure. Moreover, a preliminary pharmacophore model was built to shed light on the shift from inhibitors to activators.
Collapse
Affiliation(s)
- Cecilia Baldassarri
- Medicinal Chemistry Unit, School of Pharmacy, Chemistry Interdisciplinary Project (ChIP), University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy
| | - Gianfabio Giorgioni
- Medicinal Chemistry Unit, School of Pharmacy, Chemistry Interdisciplinary Project (ChIP), University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy
| | - Alessandro Piergentili
- Medicinal Chemistry Unit, School of Pharmacy, Chemistry Interdisciplinary Project (ChIP), University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy
| | - Wilma Quaglia
- Medicinal Chemistry Unit, School of Pharmacy, Chemistry Interdisciplinary Project (ChIP), University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy
| | - Stefano Fontana
- Center for Drug Discovery and Development-DMPK, Aptuit, an Evotec Company, Via A. Fleming 4, 37135 Verona, Italy
| | - Valerio Mammoli
- Center for Drug Discovery and Development-DMPK, Aptuit, an Evotec Company, Via A. Fleming 4, 37135 Verona, Italy
| | - Gabriele Minazzato
- Department of Agriculture, Food and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche 10, 60131 Ancona, Italy
| | - Elisa Marangoni
- Department of Agriculture, Food and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche 10, 60131 Ancona, Italy
| | - Massimiliano Gasparrini
- Department of Agriculture, Food and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche 10, 60131 Ancona, Italy
| | - Leonardo Sorci
- Division of Bioinformatics and Biochemistry, Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, 60131 Ancona, Italy
| | - Nadia Raffaelli
- Department of Agriculture, Food and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche 10, 60131 Ancona, Italy
| | - Loredana Cappellacci
- Medicinal Chemistry Unit, School of Pharmacy, Chemistry Interdisciplinary Project (ChIP), University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy
| | - Riccardo Petrelli
- Medicinal Chemistry Unit, School of Pharmacy, Chemistry Interdisciplinary Project (ChIP), University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy
| | - Fabio Del Bello
- Medicinal Chemistry Unit, School of Pharmacy, Chemistry Interdisciplinary Project (ChIP), University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy
| |
Collapse
|
46
|
Sauvey C, Meewan I, Ehrenkaufer G, Blevitt J, Jackson P, Abagyan R. High-throughput phenotypic screen identifies a new family of potent anti-amoebic compounds. PLoS One 2023; 18:e0280232. [PMID: 37159460 PMCID: PMC10168566 DOI: 10.1371/journal.pone.0280232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 12/23/2022] [Indexed: 05/11/2023] Open
Abstract
Entamoeba histolytica is a disease-causing parasitic amoeba which affects an estimated 50 million people worldwide, particularly in socioeconomically vulnerable populations experiencing water sanitation issues. Infection with E. histolytica is referred to as amoebiasis, and can cause symptoms such as colitis, dysentery, and even death in extreme cases. Drugs exist that are capable of killing this parasite, but they are hampered by downsides such as significant adverse effects at therapeutic concentrations, issues with patient compliance, the need for additional drugs to kill the transmissible cyst stage, and potential development of resistance. Past screens of small and medium sized chemical libraries have yielded anti-amoebic candidates, thus rendering high-throughput screening a promising direction for new drug discovery in this area. In this study, we screened a curated 81,664 compound library from Janssen pharmaceuticals against E. histolytica trophozoites in vitro, and from it identified a highly potent new inhibitor compound. The best compound in this series, JNJ001, showed excellent inhibition activity against E. histolytica trophozoites with EC50 values at 0.29 μM, which is better than the current approved treatment, metronidazole. Further experimentation confirmed the activity of this compound, as well as that of several structurally related compounds, originating from both the Janssen Jump-stARter library, and from chemical vendors, thus highlighting a new structure-activity relationship (SAR). In addition, we confirmed that the compound inhibited E. histolytica survival as rapidly as the current standard of care and inhibited transmissible cysts of the related model organism Entamoeba invadens. Together these results constitute the discovery of a novel class of chemicals with favorable in vitro pharmacological properties. The discovery may lead to an improved therapy against this parasite and in all of its life stages.
Collapse
Affiliation(s)
- Conall Sauvey
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School for Pharmacy and Pharmaceutical Sciences, University of California-San Diego, La Jolla, California, United States of America
| | - Ittipat Meewan
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School for Pharmacy and Pharmaceutical Sciences, University of California-San Diego, La Jolla, California, United States of America
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Gretchen Ehrenkaufer
- Division of Infectious Diseases, Department of Internal Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Jonathan Blevitt
- Janssen Research and Development, LLC, Ja Jolla, California, United States of America
| | - Paul Jackson
- Janssen Research and Development, LLC, Ja Jolla, California, United States of America
| | - Ruben Abagyan
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School for Pharmacy and Pharmaceutical Sciences, University of California-San Diego, La Jolla, California, United States of America
| |
Collapse
|
47
|
Kaczor AA, Wróbel TM, Bartuzi D. Allosteric Modulators of Dopamine D 2 Receptors for Fine-Tuning of Dopaminergic Neurotransmission in CNS Diseases: Overview, Pharmacology, Structural Aspects and Synthesis. Molecules 2022; 28:molecules28010178. [PMID: 36615372 PMCID: PMC9822192 DOI: 10.3390/molecules28010178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
Allosteric modulation of G protein-coupled receptors (GPCRs) is nowadays a hot topic in medicinal chemistry. Allosteric modulators, i.e., compounds which bind in a receptor site topologically distinct from orthosteric sites, exhibit a number of advantages. They are more selective, safer and display a ceiling effect which prevents overdosing. Allosteric modulators of dopamine D2 receptor are potential drugs against a number of psychiatric and neurological diseases, such as schizophrenia and Parkinson's disease. In this review, an insightful summary of current research on D2 receptor modulators is presented, ranging from their pharmacology and structural aspects of ligand-receptor interactions to their synthesis.
Collapse
Affiliation(s)
- Agnieszka A. Kaczor
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Medical University of Lublin, 4A Chodźki St., PL-20093 Lublin, Poland
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1, P.O. Box 1627, FI-70211 Kuopio, Finland
- Correspondence: ; Tel.: +48-81-448-72-73
| | - Tomasz M. Wróbel
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Medical University of Lublin, 4A Chodźki St., PL-20093 Lublin, Poland
| | - Damian Bartuzi
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Medical University of Lublin, 4A Chodźki St., PL-20093 Lublin, Poland
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, SE-75124 Uppsala, Sweden
| |
Collapse
|
48
|
Chang Y, Hawkins BA, Du JJ, Groundwater PW, Hibbs DE, Lai F. A Guide to In Silico Drug Design. Pharmaceutics 2022; 15:pharmaceutics15010049. [PMID: 36678678 PMCID: PMC9867171 DOI: 10.3390/pharmaceutics15010049] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/16/2022] [Accepted: 12/17/2022] [Indexed: 12/28/2022] Open
Abstract
The drug discovery process is a rocky path that is full of challenges, with the result that very few candidates progress from hit compound to a commercially available product, often due to factors, such as poor binding affinity, off-target effects, or physicochemical properties, such as solubility or stability. This process is further complicated by high research and development costs and time requirements. It is thus important to optimise every step of the process in order to maximise the chances of success. As a result of the recent advancements in computer power and technology, computer-aided drug design (CADD) has become an integral part of modern drug discovery to guide and accelerate the process. In this review, we present an overview of the important CADD methods and applications, such as in silico structure prediction, refinement, modelling and target validation, that are commonly used in this area.
Collapse
Affiliation(s)
- Yiqun Chang
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Bryson A. Hawkins
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Jonathan J. Du
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Paul W. Groundwater
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - David E. Hibbs
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Felcia Lai
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
- Correspondence:
| |
Collapse
|
49
|
Stachura DL, Nguyen S, Polyak SW, Jovcevski B, Bruning JB, Abell AD. A New 1,2,3-Triazole Scaffold with Improved Potency against Staphylococcus aureus Biotin Protein Ligase. ACS Infect Dis 2022; 8:2579-2585. [PMID: 36399035 DOI: 10.1021/acsinfecdis.2c00452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Staphylococcus aureus, a key ESKAPE bacteria, is responsible for most blood-based infections and, as a result, is a major economic healthcare burden requiring urgent attention. Here, we report in silico docking, synthesis, and assay of N1-diphenylmethyl triazole-based analogues (7-13) designed to interact with the entire binding site of S. aureus biotin protein ligase (SaBPL), an enzyme critical for the regulation of gluconeogenesis and fatty acid biosynthesis. The second aryl ring of these compounds enhances both SaBPL potency and whole cell activity against S. aureus relative to previously reported mono-benzyl triazoles. Analogues 12 and 13, with added substituents to better interact with the adenine binding site, are particularly potent, with Ki values of 6.01 ± 1.01 and 8.43 ± 0.73 nM, respectively. These analogues are the most active triazole-based inhibitors reported to date and, importantly, inhibit the growth of a clinical isolate strain of S. aureus ATCC 49775, with minimum inhibitory concentrations of 1 and 8 μg/mL, respectively.
Collapse
Affiliation(s)
- Damian L Stachura
- Department of Chemistry, School of Physical Sciences; Centre for Nanoscale BioPhotonics (CNBP) and Institute of Photonics and Advanced Sensing (IPAS), School of Biological Sciences, University of Adelaide, Adelaide5005, SA, Australia
| | - Stephanie Nguyen
- Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide5005, SA, Australia
| | - Steven W Polyak
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide5005, Australia
| | - Blagojce Jovcevski
- Department of Chemistry, School of Physical Sciences; Centre for Nanoscale BioPhotonics (CNBP) and Institute of Photonics and Advanced Sensing (IPAS), School of Biological Sciences, University of Adelaide, Adelaide5005, SA, Australia
| | - John B Bruning
- Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide5005, SA, Australia
| | - Andrew D Abell
- Department of Chemistry, School of Physical Sciences; Centre for Nanoscale BioPhotonics (CNBP) and Institute of Photonics and Advanced Sensing (IPAS), School of Biological Sciences, University of Adelaide, Adelaide5005, SA, Australia
| |
Collapse
|
50
|
Alexandrov V, Vilenchik M, Kantidze O, Tsutskiridze N, Kharchilava D, Lhewa P, Shishkin A, Gankin Y, Kirpich A. Novel Efficient Multistage Lead Optimization Pipeline Experimentally Validated for DYRK1B Selective Inhibitors. J Med Chem 2022; 65:13784-13792. [PMID: 36239428 PMCID: PMC9619999 DOI: 10.1021/acs.jmedchem.2c00988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
In addition to general challenges in drug discovery such as the
identification of lead compounds in time- and cost-effective ways,
specific challenges also exist. Particularly, it is necessary to develop
pharmacological inhibitors that effectively discriminate between closely
related molecular targets. DYRK1B kinase is considered a valuable
target for cancer-specific mono- or combination chemotherapy; however,
the inhibition of its closely related DYRK1A kinase is not beneficial.
Existing inhibitors target both kinases with essentially the same
efficiency, and the unavailability of the DYRK1B crystal structure
makes the discovery of DYRK1B-specific inhibitors even more challenging.
Here, we propose a novel multi-stage compound discovery pipeline aimed
at in silico identification of both potent and selective
small molecules from a large set of initial candidates. The method
uses structure-based docking and ligand-based quantitative structure–activity
relationship modeling. This approach allowed us to identify lead and
runner-up small-molecule compounds targeting DYRK1B with high efficiency
and specificity.
Collapse
Affiliation(s)
- Vadim Alexandrov
- Liquid Algo LLC, Hopewell Junction, New York12533, United States
| | - Maria Vilenchik
- Felicitex Therapeutics, Natick, Massachusetts01760, United States
| | - Omar Kantidze
- Quantori LLC, Cambridge, Massachusetts02142, United States
| | - Nika Tsutskiridze
- Quantori LLC, Cambridge, Massachusetts02142, United States.,Tbilisi State Medical University, Tbilisi0186, Georgia
| | - Daviti Kharchilava
- Quantori LLC, Cambridge, Massachusetts02142, United States.,Tbilisi State Medical University, Tbilisi0186, Georgia
| | - Pema Lhewa
- Department of Population Health Sciences, School of Public Health, Georgia State University, Atlanta, Georgia30303, United States
| | - Aleksandr Shishkin
- Department of Population Health Sciences, School of Public Health, Georgia State University, Atlanta, Georgia30303, United States
| | - Yuriy Gankin
- Quantori LLC, Cambridge, Massachusetts02142, United States
| | - Alexander Kirpich
- Department of Population Health Sciences, School of Public Health, Georgia State University, Atlanta, Georgia30303, United States
| |
Collapse
|