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Pallabothula VSK, Abdalrahman NT, Mori M, Fekri AH, Janďourek O, Konečná K, Paterová P, Novák M, Dudášová-Hatoková P, Štěrbová-Kovaříková P, Castellano C, Meneghetti F, Villa S, Kuneš J, Juhás M, Zitko J. A hit expansion of 3-benzamidopyrazine-2-carboxamide: Toward inhibitors of prolyl-tRNA synthetase with antimycobacterial activity. Arch Pharm (Weinheim) 2024:e2400171. [PMID: 38710636 DOI: 10.1002/ardp.202400171] [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: 03/05/2024] [Revised: 04/06/2024] [Accepted: 04/09/2024] [Indexed: 05/08/2024]
Abstract
This study presents an exploration of the chemical space around derivatives of 3-benzamidopyrazine-2-carboxamides, previously identified as potent antimycobacterial compounds with predicted binding to mycobacterial prolyl-transfer RNA synthetase. New urea derivatives (Series-1) were generally inactive, probably due to their preference for cis-trans conformation (confirmed by density functional theory calculations and experimentally by nuclear overhauser effect spectroscopy NMR). Series-2 (3-benzamidopyrazine-2-carboxamides with disubstituted benzene ring) demonstrated that substituents larger than fluorine are not tolerated in the ortho position of the benzene ring. This series brought two new compounds (21: R = 2-F, 4-Cl and 22: R = 2-F, 4-Br) with in vitro activity against Mycobacterium tuberculosis H37Rv as well as multidrug-resistant clinical isolates, with minimum inhibitory concentration ranging from 6.25 to 25 μg/mL. The lactone-type derivatives 4H-pyrazino[2,3-d][1,3]oxazin-4-ones (Series-3) were inactive, but solvent stability studies of compound 29 indicated that they might be developed to usable lactone prodrugs of inhibitors of mycobacterial aspartate decarboxylase (PanD).
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Affiliation(s)
| | | | - Matteo Mori
- Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
| | - Amir Hossein Fekri
- Department of Clinical Microbiology, University Hospital Hradec Králové, Hradec Králové, Czech Republic
| | - Ondřej Janďourek
- Department of Clinical Microbiology, University Hospital Hradec Králové, Hradec Králové, Czech Republic
| | - Klára Konečná
- Department of Clinical Microbiology, University Hospital Hradec Králové, Hradec Králové, Czech Republic
| | - Pavla Paterová
- Department of Pharmaceutical Sciences, University of Milan, Milan, Italy
| | - Martin Novák
- Biomedical Research Centre, University Hospital Hradec Králové, Hradec Králové, Czech Republic
| | - Paulína Dudášová-Hatoková
- Department of Clinical Microbiology, University Hospital Hradec Králové, Hradec Králové, Czech Republic
| | - Petra Štěrbová-Kovaříková
- Department of Clinical Microbiology, University Hospital Hradec Králové, Hradec Králové, Czech Republic
| | | | - Fiorella Meneghetti
- Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
| | - Stefania Villa
- Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
| | - Jiří Kuneš
- Department of Clinical Microbiology, University Hospital Hradec Králové, Hradec Králové, Czech Republic
| | - Martin Juhás
- Department of Clinical Microbiology, University Hospital Hradec Králové, Hradec Králové, Czech Republic
- Faculty of Science, University of Hradec Králové, Hradec Králové, Czech Republic
| | - Jan Zitko
- Department of Clinical Microbiology, University Hospital Hradec Králové, Hradec Králové, Czech Republic
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Thakur S, Mehra R. Computational Insight into Substrate-Induced Conformational Changes in Methionyl-tRNA Synthetase of Mycobacterium Tuberculosis. Protein J 2023; 42:533-546. [PMID: 37402109 DOI: 10.1007/s10930-023-10135-3] [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] [Accepted: 06/26/2023] [Indexed: 07/05/2023]
Abstract
Tuberculosis caused by Mycobacterium tuberculosis (M.tb) has killed millions worldwide. Antibiotic resistance leads to the ineffectiveness of the current therapies. Aminoacyl tRNA synthetase (aaRS) class of proteins involved in protein synthesis are promising bacterial targets for developing new therapies. Here, we carried out a systematic comparative study on the aaRS sequences from M.tb and human. We listed important M.tb aaRS that could be explored as potential M.tb targets alongside the detailed conformational space analysis of methionyl-tRNA synthetase (MetRS) in apo- and substrate-bound form, which is among the proposed targets. Understanding the conformational dynamics is central to the mechanistic understanding of MetRS, as the substrate binding leads to the conformational changes causing the reaction to proceed. We performed the most complete simulation study of M.tb MetRS for 6 microseconds (2 systems × 3 runs × 1 microsecond) in the apo and substrate-bound states. Interestingly, we observed differential features, showing comparatively large dynamics for the holo simulations, whereas the apo structures became slightly compact with reduced solvent exposed area. In contrast, the ligand size decreased significantly in holo structures possibly to relax ligand conformation. Our findings correlate with experimental studies, thus validating our protocol. Adenosine monophosphate moiety of the substrate exhibited quite higher fluctuations than the methionine. His21 and Lys54 were found to be the important residues forming prominent hydrogen bond and salt-bridge interactions with the ligand. The ligand-protein affinity decreased during simulations as computed by MMGBSA analysis over the last 500 ns trajectories, which indicates the conformational changes upon ligand binding. These differential features could be further explored for designing new M.tb inhibitors.
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Affiliation(s)
- Shivani Thakur
- Department of Chemistry, Indian Institute of Technology Bhilai, Sejbahar, Raipur, Chhattisgarh, 492015, India
| | - Rukmankesh Mehra
- Department of Chemistry, Indian Institute of Technology Bhilai, Sejbahar, Raipur, Chhattisgarh, 492015, India.
- Department of Bioscience and Biomedical Engineering, Indian Institute of Technology Bhilai, Sejbahar, Raipur, Chhattisgarh, 492015, India.
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Piña MDLN, Sahu AK, Frontera A, Biswal HS, Bauzá A. Tetrel bonds involving a CF 3 group participate in protein-drug recognition: a combined crystallographic and computational study. Phys Chem Chem Phys 2023; 25:12409-12419. [PMID: 37093130 DOI: 10.1039/d3cp00839h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
In this study, the ability of CF3 groups to bind to the electron-rich side chains and backbone groups of proteins has been investigated by combining a Protein Data Bank (PDB) survey and ab initio quantum mechanics calculations. More precisely, an inspection of the PDB involving organic ligands containing a CF3 group and electron-rich atoms (A = N, O and S) in the vicinity revealed 419 X-ray structures exhibiting CF3⋯A tetrel bonds (TtBs). In a posterior stage, those hits that exhibited the most relevant features in terms of directionality and intermolecular distance were selected for theoretical calculations at the RI-MP2/def2-TZVPD level of theory. Also, Hammett's regression plots of several TtB complexes involving meta- and para-substituted benzene derivatives were computed to shed light on the substituent effects. Moreover, the TtBs were characterized through several state-of-the-art computational techniques, such as the Quantum Theory of Atoms in Molecules (QTAIM) and Noncovalent Interactions plot (NCIplot) methodologies. We believe that the results gathered from our study will be useful for rational drug design and biological communities as well as for further expanding the role of this interaction to biomedical applications.
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Affiliation(s)
- María de Las Nieves Piña
- Department of Chemistry, Universitat de les Illes Balears, Crts de Valldemossa km 7.6, 07122 Palma de Mallorca, Baleares, Spain.
| | - Akshay Kumar Sahu
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni, Khurda, 752050, Bhubaneswar, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Crts de Valldemossa km 7.6, 07122 Palma de Mallorca, Baleares, Spain.
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni, Khurda, 752050, Bhubaneswar, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Antonio Bauzá
- Department of Chemistry, Universitat de les Illes Balears, Crts de Valldemossa km 7.6, 07122 Palma de Mallorca, Baleares, Spain.
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Cao Y, Aimaiti A, Zhu Z, Zhou L, Ye D. Discovery of Novel 3-Hydroxyquinazoline-2,4(1 H,3 H)-Dione Derivatives: A Series of Metal Ion Chelators with Potent Anti-HCV Activities. Int J Mol Sci 2022; 23:ijms23115930. [PMID: 35682608 PMCID: PMC9180926 DOI: 10.3390/ijms23115930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 05/21/2022] [Accepted: 05/24/2022] [Indexed: 11/16/2022] Open
Abstract
Millions of people worldwide suffer from acute or chronic liver inflammation caused by the hepatitis C virus (HCV). Metal ion chelators have achieved widespread success in the development of antiviral drugs. Some inhibitors with metal ion chelating structures have been proven to have good inhibitory activities on non-structural protein 5B (NS5B) polymerase. However, most of the reported metal ion chelators showed poor anti-HCV potency at the cellular level. Hence, we designed and synthesized a series of 3-hydroxyquinazoline-2,4(1H,3H)-dione derivatives with novel metal ion chelating structures. Typical compounds such as 21h, 21k, and 21t showed better anti-HCV activities than ribavirin with EC50 values less than 10 μM. 21t is currently known as one of the metal ion chelators with the best anti-HCV potency (EC50 = 2.0 μM) at the cellular level and has a better therapeutic index (TI > 25) as compared to ribavirin and the reported compound 6. In the thermal shift assay, the representative compounds 21e and 21k increased the melting temperature (Tm) of NS5B protein solution by 1.6 °C and 2.1 °C, respectively, at the test concentration, indicating that these compounds may exert an anti-HCV effect by targeting NS5B. This speculation was also supported by our molecular docking studies and ultraviolet-visible (UV-Vis) spectrophotometry assay, in which the possibility of binding of 3-hydroxyquinazoline-2,4(1H,3H)-diones with Mg2+ in the NS5B catalytic center was observed.
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Affiliation(s)
- Yang Cao
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Rd, Shanghai 201203, China; (Y.C.); (Z.Z.)
| | - Abudumijiti Aimaiti
- Shanghai Medical College, Fudan University, 130 Dongan Rd, Shanghai 200032, China;
| | - Zeyun Zhu
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Rd, Shanghai 201203, China; (Y.C.); (Z.Z.)
| | - Lu Zhou
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Rd, Shanghai 201203, China; (Y.C.); (Z.Z.)
- Correspondence: (L.Z.); (D.Y.)
| | - Deyong Ye
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Rd, Shanghai 201203, China; (Y.C.); (Z.Z.)
- Correspondence: (L.Z.); (D.Y.)
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Manickam Y, Malhotra N, Mishra S, Babbar P, Dusane A, Laleu B, Bellini V, Hakimi MA, Bougdour A, Sharma A. Double drugging of prolyl-tRNA synthetase provides a new paradigm for anti-infective drug development. PLoS Pathog 2022; 18:e1010363. [PMID: 35333915 PMCID: PMC9004777 DOI: 10.1371/journal.ppat.1010363] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 04/12/2022] [Accepted: 02/11/2022] [Indexed: 01/13/2023] Open
Abstract
Toxoplasmosis is caused by Toxoplasma gondii and in immunocompromised patients it may lead to seizures, encephalitis or death. The conserved enzyme prolyl-tRNA synthetase (PRS) is a validated druggable target in Toxoplasma gondii but the traditional ‘single target–single drug’ approach has its caveats. Here, we describe two potent inhibitors namely halofuginone (HFG) and a novel ATP mimetic (L95) that bind to Toxoplasma gondii PRS simultaneously at different neighbouring sites to cover all three of the enzyme substrate subsites. HFG and L95 act as one triple-site inhibitor in tandem and form an unusual ternary complex wherein HFG occupies the 3’-end of tRNA and the L-proline (L-pro) binding sites while L95 occupies the ATP pocket. These inhibitors exhibit nanomolar IC50 and EC50 values independently, and when given together reveal an additive mode of action in parasite inhibition assays. This work validates a novel approach and lays a structural framework for further drug development based on simultaneous targeting of multiple pockets to inhibit druggable proteins. Among infectious diseases, parasitic diseases are a major cause of death and morbidity. Toxoplasmosis is caused by an infection of the apicomplexan parasite Toxoplasma gondii. In immunocompromised patients Toxoplasmosis may lead to seizures, encephalitis or death. Novel therapeutics for human parasites are constantly needed. In recent years, the aminoacyl-tRNA synthetase (aaRS) enzyme family has been validated as a drug target for several parasitic infections. The Toxoplasma gondii prolyl-tRNA synthetase inhibitor halofuginone (HFG) has been validated earlier but here we show that an ATP-mimic called L95 is a potent inhibitor and can bind to the target enzyme in the presence of HFG. Thus, the two inhibitors described in this study simultaneously occupy all three natural substrate (ATP, L-amino acid and 3’-end of tRNA) binding pockets and thereby inhibit the enzyme leading to parasite death. This unprecedented double drugging of a pathogen enzyme may delay resistance mutation generation and this approach opens the path to multi-drugging of validated parasite proteins.
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Affiliation(s)
- Yogavel Manickam
- Molecular Medicine–Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Nipun Malhotra
- Molecular Medicine–Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Siddhartha Mishra
- Molecular Medicine–Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
- ICMR-National Institute of Malaria Research (NIMR), New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Palak Babbar
- Molecular Medicine–Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Abhishek Dusane
- Molecular Medicine–Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Benoît Laleu
- Medicines for Malaria Venture (MMV), International Center Cointrin (ICC), Geneva, Switzerland
| | - Valeria Bellini
- Institute for Advanced Biosciences (IAB), Team Host-Pathogen Interactions and Immunity to Infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Mohamed-Ali Hakimi
- Institute for Advanced Biosciences (IAB), Team Host-Pathogen Interactions and Immunity to Infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Alexandre Bougdour
- Institute for Advanced Biosciences (IAB), Team Host-Pathogen Interactions and Immunity to Infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
- * E-mail: (AB); (AS)
| | - Amit Sharma
- Molecular Medicine–Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
- ICMR-National Institute of Malaria Research (NIMR), New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- * E-mail: (AB); (AS)
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