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Prester A, Perbandt M, Galchenkova M, Oberthuer D, Werner N, Henkel A, Maracke J, Yefanov O, Hakanpää J, Pompidor G, Meyer J, Chapman H, Aepfelbacher M, Hinrichs W, Rohde H, Betzel C. Time-resolved crystallography of boric acid binding to the active site serine of the β-lactamase CTX-M-14 and subsequent 1,2-diol esterification. Commun Chem 2024; 7:152. [PMID: 38969718 PMCID: PMC11226702 DOI: 10.1038/s42004-024-01236-w] [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: 05/10/2024] [Accepted: 06/27/2024] [Indexed: 07/07/2024] Open
Abstract
The emergence and spread of antibiotic resistance represent a growing threat to public health. Of particular concern is the appearance of β-lactamases, which are capable to hydrolyze and inactivate the most important class of antibiotics, the β-lactams. Effective β-lactamase inhibitors and mechanistic insights into their action are central in overcoming this type of resistance, and in this context boronate-based β-lactamase inhibitors were just recently approved to treat multidrug-resistant bacteria. Using boric acid as a simplified inhibitor model, time-resolved serial crystallography was employed to obtain mechanistic insights into binding to the active site serine of β-lactamase CTX-M-14, identifying a reaction time frame of 80-100 ms. In a next step, the subsequent 1,2-diol boric ester formation with glycerol in the active site was monitored proceeding in a time frame of 100-150 ms. Furthermore, the displacement of the crucial anion in the active site of the β-lactamase was verified as an essential part of the binding mechanism of substrates and inhibitors. In total, 22 datasets of β-lactamase intermediate complexes with high spatial resolution of 1.40-2.04 Å and high temporal resolution range of 50-10,000 ms were obtained, allowing a detailed analysis of the studied processes. Mechanistic details captured here contribute to the understanding of molecular processes and their time frames in enzymatic reactions. Moreover, we could demonstrate that time-resolved crystallography can serve as an additional tool for identifying and investigating enzymatic reactions.
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Affiliation(s)
- Andreas Prester
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf UKE, Hamburg, Germany
- Institute of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf UKE, Hamburg, Germany
| | - Markus Perbandt
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | | | | | - Nadine Werner
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
- Centre for Integrative Biology, Department of Integrated Structural Biology, Institute of Genetics, Molecular and Cellular Biology, IGBMC, Illkirch, France
| | | | - Julia Maracke
- Center for Free-Electron Laser Science CFEL, DESY, Hamburg, Germany
| | | | | | | | - Jan Meyer
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Henry Chapman
- Center for Free-Electron Laser Science CFEL, DESY, Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging CUI, University of Hamburg, Hamburg, Germany
- Department of Physics, University of Hamburg, Hamburg, Germany
| | - Martin Aepfelbacher
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf UKE, Hamburg, Germany
| | - Winfried Hinrichs
- Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Holger Rohde
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf UKE, Hamburg, Germany.
| | - Christian Betzel
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.
- Hamburg Centre for Ultrafast Imaging CUI, University of Hamburg, Hamburg, Germany.
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2
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Behnam MAM, Klein CD. Alternate recognition by dengue protease: Proteolytic and binding assays provide functional evidence beyond an induced-fit. Biochimie 2024:S0300-9084(24)00138-X. [PMID: 38871044 DOI: 10.1016/j.biochi.2024.06.002] [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: 04/15/2024] [Revised: 05/31/2024] [Accepted: 06/10/2024] [Indexed: 06/15/2024]
Abstract
Proteases are key enzymes in viral replication, and interfering with these targets is the basis for therapeutic interventions. We previously introduced a hypothesis about conformational selection in the protease of dengue virus and related flaviviruses, based on conformational plasticity noted in X-ray structures. The present work presents the first functional evidence for alternate recognition by the dengue protease, in a mechanism based primarily on conformational selection rather than induced-fit. Recognition of distinct substrates and inhibitors in proteolytic and binding assays varies to a different extent, depending on factors reported to influence the protease structure. The pH, salinity, buffer type, and temperature cause a change in binding, proteolysis, or inhibition behavior. Using representative inhibitors with distinct structural scaffolds, we identify two contrasting binding profiles to dengue protease. Noticeable effects are observed in the binding assay upon inclusion of a non-ionic detergent in comparison to the proteolytic assay. The findings highlight the impact of the selection of testing conditions on the observed ligand affinity or inhibitory potency. From a broader scope, the dengue protease presents an example, where the induced-fit paradigm appears insufficient to explain binding events with the biological target. Furthermore, this protein reveals the complexity of comparing or combining biochemical assay data obtained under different conditions. This can be particularly critical for artificial intelligence (AI) approaches in drug discovery that rely on large datasets of compounds activity, compiled from different sources using non-identical testing procedures. In such cases, mismatched results will compromise the model quality and its predictive power.
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Affiliation(s)
- Mira A M Behnam
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
| | - Christian D Klein
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany.
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3
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Jitonnom J, Meelua W, Tue-Nguen P, Saparpakorn P, Hannongbua S, Chotpatiwetchkul W. 3D-QSAR and molecular docking studies of peptide-hybrids as dengue virus NS2B/NS3 protease inhibitors. Chem Biol Interact 2024; 396:111040. [PMID: 38735453 DOI: 10.1016/j.cbi.2024.111040] [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: 12/26/2023] [Revised: 04/11/2024] [Accepted: 05/05/2024] [Indexed: 05/14/2024]
Abstract
Global warming and climate change have made dengue disease a global health issue. More than 50 % of the world's population is at danger of dengue virus (DENV) infection, according to the World Health Organization (WHO). Therefore, a clinically approved dengue fever vaccination and effective treatment are needed. Peptide medication development is new pharmaceutical research. Here we intend to recognize the structural features inhibiting the DENV NS2B/NS3 serine protease for a series of peptide-hybrid inhibitors (R1-R2-Lys-R3-NH2) by the 3D-QSAR technique. Comparative molecular field analysis (q2 = 0.613, r2 = 0.938, r2pred = 0.820) and comparative molecular similarity indices analysis (q2 = 0.640, r2 = 0.928, r2pred = 0.693) were established, revealing minor, electropositive, H-bond acceptor groups at the R1 position, minor, electropositive, H-bond donor groups at the R2 position, and bulky, hydrophobic groups at the R3 position for higher inhibitory activity. Docking studies revealed extensive H-bond and hydrophobic interactions in the binding of tripeptide analogues to the NS2B/NS3 protease. This study provides an insight into the key structural features for the design of peptide-based inhibitors of DENV NS2B/NS3 protease.
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Affiliation(s)
- Jitrayut Jitonnom
- Unit of Excellence in Computational Molecular Science and Catalysis, University of Phayao, Phayao, 56000, Thailand; Division of Chemistry, School of Science, University of Phayao, Phayao, 56000, Thailand.
| | - Wijitra Meelua
- Unit of Excellence in Computational Molecular Science and Catalysis, University of Phayao, Phayao, 56000, Thailand; Division of Chemistry, School of Science, University of Phayao, Phayao, 56000, Thailand
| | - Panthip Tue-Nguen
- Unit of Excellence in Computational Molecular Science and Catalysis, University of Phayao, Phayao, 56000, Thailand; Program in Chemistry, Faculty of Science and Technology, Uttaradit Rajabhat University, Uttaradit, 53000, Thailand
| | | | - Supa Hannongbua
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok, 10900 Thailand
| | - Warot Chotpatiwetchkul
- Applied Computational Chemistry Research Unit, Department of Chemistry, School of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok, 10520, Thailand.
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4
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Starvaggi J, Previti S, Zappalà M, Ettari R. The Inhibition of NS2B/NS3 Protease: A New Therapeutic Opportunity to Treat Dengue and Zika Virus Infection. Int J Mol Sci 2024; 25:4376. [PMID: 38673962 PMCID: PMC11050111 DOI: 10.3390/ijms25084376] [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: 03/17/2024] [Revised: 04/12/2024] [Accepted: 04/14/2024] [Indexed: 04/28/2024] Open
Abstract
In the global pandemic scenario, dengue and zika viruses (DENV and ZIKV, respectively), both mosquito-borne members of the flaviviridae family, represent a serious health problem, and considering the absence of specific antiviral drugs and available vaccines, there is a dire need to identify new targets to treat these types of viral infections. Within this drug discovery process, the protease NS2B/NS3 is considered the primary target for the development of novel anti-flavivirus drugs. The NS2B/NS3 is a serine protease that has a dual function both in the viral replication process and in the elusion of the innate immunity. To date, two main classes of NS2B/NS3 of DENV and ZIKV protease inhibitors have been discovered: those that bind to the orthosteric site and those that act at the allosteric site. Therefore, this perspective article aims to discuss the main features of the use of the most potent NS2B/NS3 inhibitors and their impact at the social level.
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Affiliation(s)
| | | | | | - Roberta Ettari
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres 31, 98166 Messina, Italy; (J.S.); (S.P.); (M.Z.)
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5
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Zogali V, Kiousis D, Voutyra S, Kalyva G, Abdul Mahid MB, Bist P, Ki Chan KW, Vasudevan SG, Rassias G. Carbazole to indolazepinone scaffold morphing leads to potent cell-active dengue antivirals. Eur J Med Chem 2024; 268:116213. [PMID: 38382389 DOI: 10.1016/j.ejmech.2024.116213] [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: 09/26/2023] [Revised: 01/10/2024] [Accepted: 02/01/2024] [Indexed: 02/23/2024]
Abstract
According to WHO, dengue virus is classed among major threats for future pandemics and remains at large an unmet medical need as there are currently no relevant antiviral drugs whereas vaccine developments have met with safety concerns, mostly due to secondary infections caused by antibody-dependant-enhancement in cross infections among the four dengue serotypes. This adds extra complexity in dengue antiviral research and has impeded the progress in this field. Following through our previous effort which born the allosteric, dual-mode inhibitor SP-471P (a carbazole derivative, EC50 1.1 μM, CC50 100 μM) we performed further optimisation while preserving the two arylamidoxime arms and the bromoaryl domain present in SP-471P. Examination of the relative positions of these functionalities within this three-point pharmacophore ultimately led us to an indolazepinone scaffold and our lead compound SP-1769B. SP-1769B is among the most cell-efficacious against all serotypes (DENV2/3 EC50 100 nM, DENV1/4 EC50 0.95-1.25 μM) and safest (CC50 > 100 μM) anti-dengue compounds in the literature that also completely inhibits a secondary ADE-driven infection.
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Affiliation(s)
- Vasiliki Zogali
- Department of Chemistry, University of Patras, Patra, 26504, Greece
| | | | - Stefania Voutyra
- Department of Chemistry, University of Patras, Patra, 26504, Greece
| | - Georgia Kalyva
- Department of Chemistry, University of Patras, Patra, 26504, Greece
| | | | - Pradeep Bist
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road 169857, Singapore
| | - Kitti Wing Ki Chan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road 169857, Singapore
| | - Subhash G Vasudevan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road 169857, Singapore; Institute for Glycomics, Griffith University, Gold Coast Campus, QLD, 4222, Australia; Department of Microbiology and Immunology, National University of Singapore, 5 Science Drive 2, 117545, Singapore
| | - Gerasimos Rassias
- Department of Chemistry, University of Patras, Patra, 26504, Greece.
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6
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Grams RJ, Santos WL, Scorei IR, Abad-García A, Rosenblum CA, Bita A, Cerecetto H, Viñas C, Soriano-Ursúa MA. The Rise of Boron-Containing Compounds: Advancements in Synthesis, Medicinal Chemistry, and Emerging Pharmacology. Chem Rev 2024; 124:2441-2511. [PMID: 38382032 DOI: 10.1021/acs.chemrev.3c00663] [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: 02/23/2024]
Abstract
Boron-containing compounds (BCC) have emerged as important pharmacophores. To date, five BCC drugs (including boronic acids and boroles) have been approved by the FDA for the treatment of cancer, infections, and atopic dermatitis, while some natural BCC are included in dietary supplements. Boron's Lewis acidity facilitates a mechanism of action via formation of reversible covalent bonds within the active site of target proteins. Boron has also been employed in the development of fluorophores, such as BODIPY for imaging, and in carboranes that are potential neutron capture therapy agents as well as novel agents in diagnostics and therapy. The utility of natural and synthetic BCC has become multifaceted, and the breadth of their applications continues to expand. This review covers the many uses and targets of boron in medicinal chemistry.
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Affiliation(s)
- R Justin Grams
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, 900 West Campus Drive, Blacksburg, Virginia 24061, United States
| | - Webster L Santos
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, 900 West Campus Drive, Blacksburg, Virginia 24061, United States
| | | | - Antonio Abad-García
- Academia de Fisiología y Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, 11340 Mexico City, Mexico
| | - Carol Ann Rosenblum
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, 900 West Campus Drive, Blacksburg, Virginia 24061, United States
| | - Andrei Bita
- Department of Pharmacognosy & Phytotherapy, Faculty of Pharmacy, University of Medicine and Pharmacy of Craiova, 2 Petru Rareş Street, 200349 Craiova, Romania
| | - Hugo Cerecetto
- Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Mataojo 2055, 11400 Montevideo, Uruguay
| | - Clara Viñas
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Campus UAB, 08193 Bellaterra, Spain
| | - Marvin A Soriano-Ursúa
- Academia de Fisiología y Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, 11340 Mexico City, Mexico
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7
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Saleem HN, Kousar S, Jiskani AH, Sohail I, Faisal A, Saeed M. Repurposing of investigational cancer drugs: Early phase discovery of dengue virus NS2B/NS3 protease inhibitors. Arch Pharm (Weinheim) 2023; 356:e2300292. [PMID: 37582646 DOI: 10.1002/ardp.202300292] [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: 05/26/2023] [Revised: 07/29/2023] [Accepted: 07/31/2023] [Indexed: 08/17/2023]
Abstract
Dengue fever is a neglected vector-borne disease and is more prevalent in Asia. Currently, no specific treatment is available. Given the time and cost of de novo drug discovery and development, an alternative option of drug repurposing is becoming an effective tool. We screened a library of 1127 pharmacologically active, metabolically stable, and structurally diverse small anticancer molecules to identify inhibitors of the dengue virus (DENV) NS2B/NS3 protease. Enzyme kinetics and inhibition data revealed four B-cell lymphoma 2 inhibitors, that is, ABT263, ABT737, AT101, and TW37, as potent inhibitors of DENV NS2B/NS3 protease, with IC50 values of 0.86, 1.15, 0.81, and 0.89 µM, respectively. Mode of inhibition experiments and computational docking analyses indicated that ABT263 and ABT737 are competitive inhibitors, whereas AT101 and TW37 are noncompetitive inhibitors of the protease. With further evaluation, the identified inhibitors of the DENV NS2B/NS3 protease have the potential to be developed into specific anti-dengue therapeutics.
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Affiliation(s)
- Hafiza N Saleem
- Department of Chemistry and Chemical Engineering, SBA School of Science and Engineering, Lahore University of Management Sciences (LUMS), Lahore, Pakistan
| | - Summara Kousar
- Department of Chemistry and Chemical Engineering, SBA School of Science and Engineering, Lahore University of Management Sciences (LUMS), Lahore, Pakistan
| | - Ammar Hassan Jiskani
- Department of Chemistry and Chemical Engineering, SBA School of Science and Engineering, Lahore University of Management Sciences (LUMS), Lahore, Pakistan
| | - Iqra Sohail
- Department of Life Sciences, SBA School of Science and Engineering, Lahore University of Management Sciences (LUMS), Lahore, Pakistan
| | - Amir Faisal
- Department of Life Sciences, SBA School of Science and Engineering, Lahore University of Management Sciences (LUMS), Lahore, Pakistan
| | - Muhammad Saeed
- Department of Chemistry and Chemical Engineering, SBA School of Science and Engineering, Lahore University of Management Sciences (LUMS), Lahore, Pakistan
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8
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Urmi UL, Attard S, Vijay AK, Willcox MDP, Kumar N, Islam S, Kuppusamy R. Antiviral Activity of Anthranilamide Peptidomimetics against Herpes Simplex Virus 1 and a Coronavirus. Antibiotics (Basel) 2023; 12:1436. [PMID: 37760732 PMCID: PMC10525570 DOI: 10.3390/antibiotics12091436] [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: 08/27/2023] [Revised: 09/08/2023] [Accepted: 09/10/2023] [Indexed: 09/29/2023] Open
Abstract
The development of potent antiviral agents is of utmost importance to combat the global burden of viral infections. Traditional antiviral drug development involves targeting specific viral proteins, which may lead to the emergence of resistant strains. To explore alternative strategies, we investigated the antiviral potential of antimicrobial peptidomimetic compounds. In this study, we evaluated the antiviral potential of 17 short anthranilamide-based peptidomimetic compounds against two viruses: Murine hepatitis virus 1 (MHV-1) which is a surrogate of human coronaviruses and herpes simplex virus 1 (HSV-1). The half-maximal inhibitory concentration (IC50) values of these compounds were determined in vitro to assess their potency as antiviral agents. Compounds 11 and 14 displayed the most potent inhibitory effects with IC50 values of 2.38 μM, and 6.3 μM against MHV-1 while compounds 9 and 14 showed IC50 values of 14.8 μM and 13 μM against HSV-1. Multiple antiviral assessments and microscopic images obtained through transmission electron microscopy (TEM) collectively demonstrated that these compounds exert a direct influence on the viral envelope. Based on this outcome, it can be concluded that peptidomimetic compounds could offer a new approach for the development of potent antiviral agents.
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Affiliation(s)
- Umme Laila Urmi
- School of Optometry and Vision Science, University of New South Wales, Sydney, NSW 2052, Australia; (A.K.V.); (S.I.); (R.K.)
| | - Samuel Attard
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia; (S.A.); (N.K.)
| | - Ajay Kumar Vijay
- School of Optometry and Vision Science, University of New South Wales, Sydney, NSW 2052, Australia; (A.K.V.); (S.I.); (R.K.)
| | - Mark D. P. Willcox
- School of Optometry and Vision Science, University of New South Wales, Sydney, NSW 2052, Australia; (A.K.V.); (S.I.); (R.K.)
| | - Naresh Kumar
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia; (S.A.); (N.K.)
| | - Salequl Islam
- School of Optometry and Vision Science, University of New South Wales, Sydney, NSW 2052, Australia; (A.K.V.); (S.I.); (R.K.)
- Department of Microbiology, Jahangirnagar University, Savar 1342, Bangladesh
| | - Rajesh Kuppusamy
- School of Optometry and Vision Science, University of New South Wales, Sydney, NSW 2052, Australia; (A.K.V.); (S.I.); (R.K.)
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia; (S.A.); (N.K.)
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9
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Ng R, Zhang G, Li JJ. An update on the discovery and development of reversible covalent inhibitors. Med Chem Res 2023; 32:1039-1062. [PMID: 37305209 PMCID: PMC10148018 DOI: 10.1007/s00044-023-03065-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 04/18/2023] [Indexed: 06/13/2023]
Abstract
Small molecule drugs that covalently bind irreversibly to their target proteins have several advantages over conventional reversible inhibitors. They include increased duration of action, less-frequent drug dosing, reduced pharmacokinetic sensitivity, and the potential to target intractable shallow binding sites. Despite these advantages, the key challenges of irreversible covalent drugs are their potential for off-target toxicities and immunogenicity risks. Incorporating reversibility into covalent drugs would lead to less off-target toxicity by forming reversible adducts with off-target proteins and thus reducing the risk of idiosyncratic toxicities caused by the permanent modification of proteins, which leads to higher levels of potential haptens. Herein, we systematically review electrophilic warheads employed during the development of reversible covalent drugs. We hope the structural insights of electrophilic warheads would provide helpful information to medicinal chemists and aid in designing covalent drugs with better on-target selectivity and improved safety. Graphical Abstract
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Affiliation(s)
- Raymond Ng
- Olema Oncology, 512 2nd St., 4th Floor, San Francisco, 94107 CA USA
| | - Guiping Zhang
- Genhouse Bio, No.1 Xinze Road, Suzhou Industrial Park, Suzhou, Jiangsu Province 215123 PR China
| | - Jie Jack Li
- Genhouse Bio, No.1 Xinze Road, Suzhou Industrial Park, Suzhou, Jiangsu Province 215123 PR China
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10
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Ding D, Xu S, da Silva-Júnior EF, Liu X, Zhan P. Medicinal chemistry insights into antiviral peptidomimetics. Drug Discov Today 2023; 28:103468. [PMID: 36528280 DOI: 10.1016/j.drudis.2022.103468] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 12/06/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022]
Abstract
The (re)emergence of multidrug-resistant viruses and the emergence of new viruses highlight the urgent and ongoing need for new antiviral agents. The use of peptidomimetics as therapeutic drugs has often been associated with advantages, such as enhanced binding affinity, improved metabolic stability, and good bioavailability profiles. The development of novel antivirals is currently driven by strategies of converting peptides into peptidomimetic derivatives. In this review, we outline different structural modification design strategies for developing novel peptidomimetics as antivirals, involving N- or C-cap terminal structure modifications, pseudopeptides, amino acid modifications, inverse-peptides, cyclization, and molecular hybridization. We also present successful recent examples of peptidomimetic designs.
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Affiliation(s)
- Dang Ding
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Shujing Xu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, 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, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China.
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China.
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11
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Braun NJ, Huber S, Schmacke LC, Heine A, Steinmetzer T. Boroleucine-Derived Covalent Inhibitors of the ZIKV Protease. ChemMedChem 2023; 18:e202200336. [PMID: 36325810 PMCID: PMC10100045 DOI: 10.1002/cmdc.202200336] [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: 06/24/2022] [Revised: 11/02/2022] [Indexed: 11/06/2022]
Abstract
The Zika virus (ZIKV) remains a potential threat to the public health due to the lack of both an approved vaccination or a specific treatment. In this work, a series of peptidic inhibitors of the ZIKV protease with boroleucine as P1 residue was synthesized. The highest affinities with Ki values down to 8 nM were observed for compounds with basic residues in both P2 and P3 position and at the N-terminus. The low potency of reference compounds containing leucine, leucine-amide or isopentylamide as P1 residue suggested a covalent binding mode of the boroleucine-derived inhibitors. This was finally proven by crystal structure determination of the most potent inhibitor from this series in complex with the ZIKV protease.
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Affiliation(s)
- Niklas J Braun
- Institute of Pharmaceutical Chemistry, Philipps University of Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Simon Huber
- Institute of Pharmaceutical Chemistry, Philipps University of Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Luna C Schmacke
- Institute of Pharmaceutical Chemistry, Philipps University of Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Andreas Heine
- Institute of Pharmaceutical Chemistry, Philipps University of Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Torsten Steinmetzer
- Institute of Pharmaceutical Chemistry, Philipps University of Marburg, Marbacher Weg 6, 35032, Marburg, Germany
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12
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Zephyr J, Rao DN, Johnson C, Shaqra AM, Nalivaika EA, Jordan A, Kurt Yilmaz N, Ali A, Schiffer CA. Allosteric quinoxaline-based inhibitors of the flavivirus NS2B/NS3 protease. Bioorg Chem 2023; 131:106269. [PMID: 36446201 PMCID: PMC10155214 DOI: 10.1016/j.bioorg.2022.106269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/27/2022] [Accepted: 11/06/2022] [Indexed: 11/20/2022]
Abstract
Viruses from the Flavivirus genus infect millions of people worldwide and cause severe diseases, including recent epidemics of dengue virus (DENV), and Zika virus (ZIKV). There is currently no antiviral treatment against flavivirus infections, despite considerable efforts to develop inhibitors against essential viral enzymes including NS2B/NS3 protease. Targeting the flavivirus NS2B/NS3 protease proved to be challenging because of the conformational dynamics, topology, and electrostatic properties of the active site. Here, we report the identification of quinoxaline-based allosteric inhibitors by fragment-based drug discovery approach as a promising new drug-like scaffold to target the NS2B/NS3 protease. Enzymatic assays and mutational analysis of the allosteric site in ZIKV NS2B/NS3 protease support noncompetitive inhibition mechanism as well as engineered DENV protease construct indicating the compounds likely compete with the NS2B cofactor for binding to the protease domain. Furthermore, antiviral activity confirmed the therapeutic potential of this new inhibitor scaffold.
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Affiliation(s)
- Jacqueto Zephyr
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, United States
| | - Desaboini Nageswara Rao
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, United States
| | - Colby Johnson
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, United States
| | - Ala M Shaqra
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, United States
| | - Ellen A Nalivaika
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, United States
| | - Aria Jordan
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, United States
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, United States.
| | - Akbar Ali
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, United States.
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, United States.
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13
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Santos LH, Caffarena ER, Ferreira RS. pH and non-covalent ligand binding modulate Zika virus NS2B/NS3 protease binding site residues: Discoveries from MD and constant pH MD simulations. J Biomol Struct Dyn 2022; 40:10359-10372. [PMID: 34180376 DOI: 10.1080/07391102.2021.1943528] [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] [Indexed: 12/16/2022]
Abstract
Zika virus (ZIKV) is a global health concern and has been linked to severe neurological pathologies. Although no medication is available yet, many efforts to develop antivirals and host cell binding inhibitors led to attractive drug-like scaffolds, mainly targeting the nonstructural NS2B/NS3 protease (NS2B/NS3pro). NS2B/NS3pro active site has several titratable residues susceptible to pH changes and ligand binding; hence, understanding these residues' protonation is essential to drug design efforts targeting the active site. Here we use in silico methods to probe non-covalent binding and its effect on pKa shifts of the active site residues on a ligand-free protease and with a non-peptidic competitive inhibitor (Ki=13.5 µM). By applying constant pH molecular dynamics, we found that the catalytic residues of the unbound NS2B/NS3pro achieved the protonation needed for the serine protease mechanism over the pH value of 8.5. Nevertheless, the protease in the holo state achieved this same scenario at lower pH values. Also, non-covalent binding affected the catalytic triad (H51, D75, and S135) by stabilizing their distances and interaction network. Thus, NS2B/NS3pro residues configuration for activity might be both pH-dependent and influenced by ligand binding. However, compound presence within the binding site destabilized the NS2B, interfering with the closed and active conformation necessary for substrate binding and catalysis. Our outcomes provide valuable insights into non-covalent inhibitor behavior and its effect on protease active site residues, impacting optimization and design of novel compounds. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Lucianna H Santos
- Laboratório de Modelagem Molecular e Planejamento de Fármacos, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ernesto R Caffarena
- Grupo de Biofísica Computacional e Modelagem Molecular, Programa de Computação Científica, Fiocruz, Rio de Janeiro, Brazil
| | - Rafaela S Ferreira
- Laboratório de Modelagem Molecular e Planejamento de Fármacos, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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14
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Wang S, Ren Y, Wang Z, Jiang X, Xu S, Zhang X, Zhao S, Zalloum WA, Liu X, Zhan P. The current progress in the use of boron as a platform for novel antiviral drug design. Expert Opin Drug Discov 2022; 17:1329-1340. [PMID: 36448326 DOI: 10.1080/17460441.2023.2153829] [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: 12/02/2022]
Abstract
INTRODUCTION Boron has attracted extensive interest due to several FDA-approved boron-containing drugs and other pharmacological agents in clinical trials. As a semimetal, it has peculiar biochemical characteristics which could be utilized in designing novel drugs against drug-resistant viruses. Emerging and reemerging viral pandemics are major threats to human health. Accordingly, we aim to comprehensively review the current status of antiviral boron-containing compounds. AREAS COVERED This review focuses on the utilization of boron to design molecules against viruses from two perspectives: (i) single boron atom-containing compounds acting on miscellaneous viral targets and (ii) boron clusters. The peculiar properties of antiviral boron-containing compounds and their diverse binding modes with viral targets are described in detail in this review. EXPERT OPINION Compounds bearing boronic acid can interact with viral targets by forming covalent or robust hydrogen bonds. This feature is valuable for combating resistant viruses. Furthermore, boron clusters can form dihydrogen bonds and bear features such as three-dimensional aromaticity, hydrophobicity, and biological stability. All these features demonstrated boron as a probable essential element with immense potential for drug design.
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Affiliation(s)
- Shuo Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, PR China
| | - Yujie Ren
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, PR China
| | - Zhao Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, PR China
| | - Xiangyi Jiang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, PR China
| | - Shujing Xu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, PR China
| | - Xujie Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, PR China
| | - Shujie Zhao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, PR China
| | - Waleed A Zalloum
- Department of Pharmacy, Faculty of Health Science, American University of Madaba, P.O Box 2882 11821, Amman, Jordan
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, PR China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, PR China
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15
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Wang S, Ren Y, Li Q, Wang Y, Jiang X, Xu S, Zhang X, Zhao S, Bradley DP, Woodson ME, Zhao F, Wu S, Li Y, Tian Y, Liu X, Tavis JE, Zhan P. Design, synthesis, and biological evaluation of novel sulfamoylbenzamide derivatives as HBV capsid assembly modulators. Bioorg Chem 2022; 129:106192. [PMID: 36265355 PMCID: PMC10591450 DOI: 10.1016/j.bioorg.2022.106192] [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] [Received: 09/13/2022] [Revised: 09/25/2022] [Accepted: 10/01/2022] [Indexed: 11/02/2022]
Abstract
Capsid assembly modulators (CAMs) represent a novel class of antiviral agents targeting hepatitis B virus (HBV) capsid to disrupt the assembly process. NVR 3-778 is the first CAM to demonstrate antiviral activity in patients infected with HBV. However, the relatively low aqueous solubility and moderate activity in the human body halted further development of NVR 3-778. To improve the anti-HBV activity and the drug-like properties of NVR 3-778, we designed and synthesized a series of NVR 3-778 derivatives. Notably, phenylboronic acid-bearing compound 7b (EC50 = 0.83 ± 0.33 µM, CC50 = 19.4 ± 5.0 µM) displayed comparable anti-HBV activity to NVR 3-778 (EC50 = 0.73 ± 0.20 µM, CC50 = 23.4 ± 7.0 µM). Besides, 7b showed improved water solubility (328.8 µg/mL, pH 7) compared to NVR 3-778 (35.8 µg/mL, pH 7). Size exclusion chromatography (SEC) and quantification of encapsidated viral RNA were used to demonstrate that 7b behaves as a class II CAM similar to NVR 3-778. Moreover, molecular dynamics (MD) simulations were conducted to rationalize the structure-activity relationships (SARs) of these novel derivatives and to understand their key interactions with the binding pocket, which provide useful indications for guiding the further rational design of more effective anti-HBV drugs.
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Affiliation(s)
- Shuo Wang
- 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
| | - Yujie Ren
- 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
| | - Qilan Li
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, 1100, S. Grand Blvd, St. Louis, MO 63104, USA
| | - Ya Wang
- CAMS Key Laboratory of Antiviral Drug Research, Beijing Key Laboratory of Antimicrobial Agents, NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100050 Beijing, PR China
| | - Xiangyi Jiang
- 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
| | - Shujing Xu
- 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
| | - 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
| | - Daniel P Bradley
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, 1100, S. Grand Blvd, St. Louis, MO 63104, USA
| | - Molly E Woodson
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, 1100, S. Grand Blvd, St. Louis, MO 63104, USA
| | - Fabao 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
| | - Shuo Wu
- CAMS Key Laboratory of Antiviral Drug Research, Beijing Key Laboratory of Antimicrobial Agents, NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100050 Beijing, PR China
| | - Yuhuan Li
- CAMS Key Laboratory of Antiviral Drug Research, Beijing Key Laboratory of Antimicrobial Agents, NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100050 Beijing, PR China
| | - Ye Tian
- 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.
| | - John E Tavis
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, 1100, S. Grand Blvd, St. Louis, MO 63104, USA.
| | - 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.
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16
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Deng L, Mo J, Zhang Y, Peng K, Li H, Ouyang S, Feng Z, Fang W, Wei J, Rong D, Zhang X, Wang Y. Boronic Acid: A Novel Pharmacophore Targeting Src Homology 2 (SH2) Domain of STAT3. J Med Chem 2022; 65:13094-13111. [PMID: 36170649 DOI: 10.1021/acs.jmedchem.2c00940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
SH2 domains have been recognized as promising targets for various human diseases. However, targeting SH2 domains with phosphopeptides or small-molecule inhibitors derived from bioisosteres of the phosphate group is still challenging. Identifying novel bioisosteres of the phosphate group to achieve favorable in vivo potency is urgently needed. Here, we report the feasibility of targeting the STAT3-SH2 domain with a boronic acid group and the identification of a highly potent inhibitor compound 7 by replacing the carboxylic acid of compound 4 with a boronic acid. Compound 7 shows higher binding affinity, better cellular potency, more favorable PK profiles, and higher in vivo antitumor activity than 4. The stronger anticancer effect of 7 partially stems from its covalent binding mode with the SH2 domain, verified by the washout experiments. The relatively high level of sequence conservation among SH2 domains makes the results presented here of general significance.
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Affiliation(s)
- Lin Deng
- Balance-Based Drug Discovery Laboratory (BBDDL), School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Jianshan Mo
- National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Yi Zhang
- Balance-Based Drug Discovery Laboratory (BBDDL), School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Keren Peng
- National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Huaxuan Li
- Balance-Based Drug Discovery Laboratory (BBDDL), School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Shumin Ouyang
- National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Zongbo Feng
- Balance-Based Drug Discovery Laboratory (BBDDL), School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Wei Fang
- Balance-Based Drug Discovery Laboratory (BBDDL), School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Jianwei Wei
- Balance-Based Drug Discovery Laboratory (BBDDL), School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Deqin Rong
- Balance-Based Drug Discovery Laboratory (BBDDL), School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Xiaolei Zhang
- National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Yuanxiang Wang
- Balance-Based Drug Discovery Laboratory (BBDDL), School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China.,National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
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17
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Jonniya NA, Kar P. Functional Loop Dynamics and Characterization of the Inactive State of the NS2B-NS3 Dengue Protease due to Allosteric Inhibitor Binding. J Chem Inf Model 2022; 62:3800-3813. [PMID: 35950997 DOI: 10.1021/acs.jcim.2c00461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dengue virus, a flavivirus that causes dengue shock syndrome and dengue hemorrhagic fever, is currently prevalent worldwide. A two-component protease (NS2B-NS3) is essential for maturation, representing an important target for designing anti-flavivirus drugs. Previously, consideration has been centered on developing active-site inhibitors of NS2B-NS3pro. However, the flat and charged nature of its active site renders difficulties in developing inhibitors, suggesting an alternative strategy for identifying allosteric inhibitors. The allosterically sensitive site of the dengue protease is located near Ala125, between the 120s loop and 150s loop. Using atomistic molecular dynamics simulations, we have explored the protease's conformational dynamics upon binding of an allosteric inhibitor. Furthermore, characterization of the inherent flexible loops (71-75s loop, 120s loop, and 150s loop) is carried out for allosteric-inhibitor-bound wild-type and mutant A125C variants and a comparison is performed with its unbound state to extract the structural changes describing the inactive state of the protease. Our study reveals that compared to the unliganded system, the inhibitor-bound system shows large structural changes in the 120s loop and 150s loop in contrast to the rigid 71-75s loop. The unliganded system shows a closed-state pocket in contrast to the open state for the wild-type complex that locks the protease into the open and inactive-state conformations. However, the mutant complex fluctuates between open and closed states. Also, we tried to see how mutation and binding of an allosteric inhibitor perturb the connectivity in a protein structure network (PSN) at contact levels. Altogether, our study reveals the mechanism of conformational rearrangements of loops at the molecular level, locking the protein in an inactive conformation, which may be useful for developing allosteric inhibitors.
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Affiliation(s)
- Nisha Amarnath Jonniya
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Indore, Madhya Pradesh 453552, India
| | - Parimal Kar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Indore, Madhya Pradesh 453552, India
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18
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Kühl N, Lang J, Leuthold MM, Klein CD. Discovery of potent benzoxaborole inhibitors against SARS-CoV-2 main and dengue virus proteases. Eur J Med Chem 2022; 240:114585. [PMID: 35863275 PMCID: PMC9272583 DOI: 10.1016/j.ejmech.2022.114585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/08/2022] [Accepted: 06/20/2022] [Indexed: 11/04/2022]
Abstract
The RNA viruses SARS-CoV-2 and dengue pose a major threat to human health worldwide and their proteases (Mpro; NS2B/NS3) are considered as promising targets for drug development. We present the synthesis and biological evaluation of novel benzoxaborole inhibitors of these two proteases. The most active compound achieves single-digit micromolar activity against SARS-CoV-2 Mpro in a biochemical assay. The most active substance against dengue NS2B/NS3 protease has submicromolar activity in cells (EC50 0.54 μM) and inhibits DENV-2 replication in cell culture. Most benzoxaboroles had no relevant cytotoxicity or significant off-target inhibition. Furthermore, the class demonstrated passive membrane penetration and stability against the evaluated proteases. This compound class may contribute to the development of antiviral agents with activity against DENV or SARS-CoV-2.
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Affiliation(s)
- Nikos Kühl
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
| | - Johannes Lang
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
| | - Mila M Leuthold
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
| | - Christian D Klein
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany.
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19
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Qian X, Qi Z. Mosquito-Borne Flaviviruses and Current Therapeutic Advances. Viruses 2022; 14:v14061226. [PMID: 35746697 PMCID: PMC9229039 DOI: 10.3390/v14061226] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/25/2022] [Accepted: 06/02/2022] [Indexed: 12/10/2022] Open
Abstract
Mosquito-borne flavivirus infections affect approximately 400 million people worldwide each year and are global threats to public health. The common diseases caused by such flaviviruses include West Nile, yellow fever, dengue, Zika infection and Japanese encephalitis, which may result in severe symptoms and disorders of multiple organs or even fatal outcomes. Till now, no specific antiviral agents are commercially available for the treatment of the diseases. Numerous strategies have been adopted to develop novel and promising inhibitors against mosquito-borne flaviviruses, including drugs targeting the critical viral components or essential host factors during infection. Research advances in antiflaviviral therapy might optimize and widen the treatment options for flavivirus infection. This review summarizes the current developmental progresses and involved molecular mechanisms of antiviral agents against mosquito-borne flaviviruses.
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20
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Mirza MU, Alanko I, Vanmeert M, Muzzarelli KM, Salo-Ahen OMH, Abdullah I, Kovari IA, Claes S, De Jonghe S, Schols D, Schinazi RF, Kovari LC, Trant JF, Ahmad S, Froeyen M. The discovery of Zika virus NS2B-NS3 inhibitors with antiviral activity via an integrated virtual screening approach. Eur J Pharm Sci 2022; 175:106220. [PMID: 35618201 DOI: 10.1016/j.ejps.2022.106220] [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: 03/22/2022] [Revised: 05/18/2022] [Accepted: 05/23/2022] [Indexed: 11/15/2022]
Abstract
With expanding recent outbreaks and a lack of treatment options, the Zika virus (ZIKV) poses a severe health concern. The availability of ZIKV NS2B-NS3 co-crystallized structures paved the way for rational drug discovery. A computer-aided structure-based approach was used to screen a diverse library of compounds against ZIKV NS2B-NS3 protease. The top hits were selected based on various binding free energy calculations followed by per-residue decomposition analysis. The selected hits were then evaluated for their biological potential with ZIKV protease inhibition assay and antiviral activity. Among 26 selected compounds, 8 compounds showed promising activity against ZIKV protease with a percentage inhibition of greater than 25 and 3 compounds displayed ∼50% at 10 µM, which indicates an enrichment rate of approximately 36% (threshold IC50 < 10 µM) in the ZIKV-NS2B-NS3 protease inhibition assay. Of these, only one compound (23) produced whole-cell anti-ZIKV activity, and the binding mode of 23 was extensively analyzed through long-run molecular dynamics simulations. The current study provides a promising starting point for the further development of novel compounds against ZIKV.
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Affiliation(s)
- Muhammad Usman Mirza
- KU Leuven, Rega Institute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences, Medicinal Chemistry, Herestraat 49, box 1041, Leuven 3000, Belgium; Department of Chemistry and Biochemistry, University of Windsor, Windsor N9B 3P4, ON, Canada
| | - Ida Alanko
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, FI-20520 Turku, Finland; Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, FI-20520 Turku, Finland
| | - Michiel Vanmeert
- KU Leuven, Rega Institute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences, Medicinal Chemistry, Herestraat 49, box 1041, Leuven 3000, Belgium
| | - Kendall M Muzzarelli
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit 48201, MI, USA
| | - Outi M H Salo-Ahen
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, FI-20520 Turku, Finland; Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, FI-20520 Turku, Finland
| | - Iskandar Abdullah
- Drug Design Development Research Group, Department of Chemistry, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Iulia A Kovari
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit 48201, MI, USA
| | - Sandra Claes
- KU Leuven, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Herestraat 49, box 1043, Leuven, Belgium
| | - Steven De Jonghe
- KU Leuven, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Herestraat 49, box 1043, Leuven, Belgium
| | - Dominique Schols
- KU Leuven, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Herestraat 49, box 1043, Leuven, Belgium
| | - Raymond F Schinazi
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta 30322, GA, USA
| | - Ladislau C Kovari
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit 48201, MI, USA
| | - John F Trant
- Department of Chemistry and Biochemistry, University of Windsor, Windsor N9B 3P4, ON, Canada
| | - Sarfraz Ahmad
- Drug Design Development Research Group, Department of Chemistry, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Matheus Froeyen
- KU Leuven, Rega Institute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences, Medicinal Chemistry, Herestraat 49, box 1041, Leuven 3000, Belgium.
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21
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Qiu SB, Xiao JH, Chen PR, Ai KL, Pan KL, Chen JK, Chen YW, Pan PS. Robust Synthesis of Tetra‐Boronate Esters Analogues and the Corresponding Boronic Acids Derivatives. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Shuo-Bei Qiu
- National Defense Medical Center Institute of Life Sciences TAIWAN
| | | | - Pin-Rui Chen
- Tamkang University Department of Chemistry TAIWAN
| | - Kuan-Lin Ai
- Tamkang University Department of Chemistry TAIWAN
| | - Kuan-Lin Pan
- Tamkang University Department of Chemistry TAIWAN
| | - Jen-Kun Chen
- National Health Research Institutes Institute of Biomedical Engineering and Nanomedicine TAIWAN
| | - Yi-Wei Chen
- Taipei Veterans General Hospital Oncology New Taipei City TAIWAN
| | - Po-Shen Pan
- Tamkang University Chemistry No.151, Yingzhuan Rd., Tamsui Dist., 25137 New Taipei City TAIWAN
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22
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Huber S, Braun NJ, Schmacke LC, Quek JP, Murra R, Bender D, Hildt E, Luo D, Heine A, Steinmetzer T. Structure-Based Optimization and Characterization of Macrocyclic Zika Virus NS2B-NS3 Protease Inhibitors. J Med Chem 2022; 65:6555-6572. [PMID: 35475620 DOI: 10.1021/acs.jmedchem.1c01860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Zika virus (ZIKV) is a human pathogenic arbovirus. So far, neither a specific treatment nor a vaccination against ZIKV infections has been approved. Starting from our previously described lead structure, a series of 29 new macrocyclic inhibitors of the Zika virus protease containing different linker motifs have been synthesized. By selecting hydrophobic d-amino acids as part of the linker, numerous inhibitors with Ki values < 5 nM were obtained. For 12 inhibitors, crystal structures in complex with the ZIKV protease up to 1.30 Å resolution were determined, which contribute to the understanding of the observed structure-activity relationship (SAR). In immunofluorescence assays, an antiviral effect was observed for compound 26 containing a d-homocyclohexylalanine residue in its linker segment. Due to its excellent selectivity profile and low cytotoxicity, this inhibitor scaffold could be a suitable starting point for the development of peptidic drugs against the Zika virus and related flaviviruses.
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Affiliation(s)
- Simon Huber
- Institute of Pharmaceutical Chemistry, Philipps University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Niklas J Braun
- Institute of Pharmaceutical Chemistry, Philipps University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Luna C Schmacke
- Institute of Pharmaceutical Chemistry, Philipps University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Jun Ping Quek
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921.,NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921
| | - Robin Murra
- Federal Institute for Vaccines and Biomedicines, Department of Virology, Paul-Ehrlich-Institut, Paul-Ehrlich-Straße 51-59, 63225 Langen, Germany
| | - Daniela Bender
- Federal Institute for Vaccines and Biomedicines, Department of Virology, Paul-Ehrlich-Institut, Paul-Ehrlich-Straße 51-59, 63225 Langen, Germany
| | - Eberhard Hildt
- Federal Institute for Vaccines and Biomedicines, Department of Virology, Paul-Ehrlich-Institut, Paul-Ehrlich-Straße 51-59, 63225 Langen, Germany
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921.,NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Andreas Heine
- Institute of Pharmaceutical Chemistry, Philipps University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Torsten Steinmetzer
- Institute of Pharmaceutical Chemistry, Philipps University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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23
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Das BC, Nandwana NK, Das S, Nandwana V, Shareef MA, Das Y, Saito M, Weiss LM, Almaguel F, Hosmane NS, Evans T. Boron Chemicals in Drug Discovery and Development: Synthesis and Medicinal Perspective. Molecules 2022; 27:2615. [PMID: 35565972 PMCID: PMC9104566 DOI: 10.3390/molecules27092615] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/11/2022] [Accepted: 04/14/2022] [Indexed: 02/06/2023] Open
Abstract
A standard goal of medicinal chemists has been to discover efficient and potent drug candidates with specific enzyme-inhibitor abilities. In this regard, boron-based bioactive compounds have provided amphiphilic properties to facilitate interaction with protein targets. Indeed, the spectrum of boron-based entities as drug candidates against many diseases has grown tremendously since the first clinically tested boron-based drug, Velcade. In this review, we collectively represent the current boron-containing drug candidates, boron-containing retinoids, benzoxaboroles, aminoboronic acid, carboranes, and BODIPY, for the treatment of different human diseases.In addition, we also describe the synthesis, key structure-activity relationship, and associated biological activities, such as antimicrobial, antituberculosis, antitumor, antiparasitic, antiprotozoal, anti-inflammatory, antifolate, antidepressant, antiallergic, anesthetic, and anti-Alzheimer's agents, as well as proteasome and lipogenic inhibitors. This compilation could be very useful in the exploration of novel boron-derived compounds against different diseases, with promising efficacy and lesser side effects.
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Affiliation(s)
- Bhaskar C. Das
- Arnold and Marie Schwartz College of Pharmacy and Health Sciences, Long Island University, Brooklyn, NY 11201, USA; (N.K.N.); (S.D.); (V.N.); (M.A.S.)
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Surgery, Weill Cornell Medical College, Cornell University, New York, NY 10065, USA;
| | - Nitesh K. Nandwana
- Arnold and Marie Schwartz College of Pharmacy and Health Sciences, Long Island University, Brooklyn, NY 11201, USA; (N.K.N.); (S.D.); (V.N.); (M.A.S.)
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sasmita Das
- Arnold and Marie Schwartz College of Pharmacy and Health Sciences, Long Island University, Brooklyn, NY 11201, USA; (N.K.N.); (S.D.); (V.N.); (M.A.S.)
| | - Varsha Nandwana
- Arnold and Marie Schwartz College of Pharmacy and Health Sciences, Long Island University, Brooklyn, NY 11201, USA; (N.K.N.); (S.D.); (V.N.); (M.A.S.)
| | - Mohammed Adil Shareef
- Arnold and Marie Schwartz College of Pharmacy and Health Sciences, Long Island University, Brooklyn, NY 11201, USA; (N.K.N.); (S.D.); (V.N.); (M.A.S.)
| | - Yogarupa Das
- Nathan S. Kline Institute for Psychiatric Research, Orangeburg, NY 10962, USA; (Y.D.); (M.S.)
| | - Mariko Saito
- Nathan S. Kline Institute for Psychiatric Research, Orangeburg, NY 10962, USA; (Y.D.); (M.S.)
| | - Louis M. Weiss
- Department of Pathology, Division of Parasitology and Tropical Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA;
| | - Frankis Almaguel
- School of Medicine, Loma Linda University Health, Loma Linda, CA 92350, USA;
| | - Narayan S. Hosmane
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA;
| | - Todd Evans
- Department of Surgery, Weill Cornell Medical College, Cornell University, New York, NY 10065, USA;
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24
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Discovery of Bispecific Lead Compounds from Azadirachta indica against ZIKA NS2B-NS3 Protease and NS5 RNA Dependent RNA Polymerase Using Molecular Simulations. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27082562. [PMID: 35458761 PMCID: PMC9025849 DOI: 10.3390/molecules27082562] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/12/2022] [Accepted: 04/13/2022] [Indexed: 12/30/2022]
Abstract
Zika virus (ZIKV) has been characterized as one of many potential pathogens and placed under future epidemic outbreaks by the WHO. However, a lack of potential therapeutics can result in an uncontrolled pandemic as with other human pandemic viruses. Therefore, prioritized effective therapeutics development has been recommended against ZIKV. In this context, the present study adopted a strategy to explore the lead compounds from Azadirachta indica against ZIKV via concurrent inhibition of the NS2B-NS3 protease (ZIKVpro) and NS5 RNA dependent RNA polymerase (ZIKVRdRp) proteins using molecular simulations. Initially, structure-based virtual screening of 44 bioflavonoids reported in Azadirachta indica against the crystal structures of targeted ZIKV proteins resulted in the identification of the top four common bioflavonoids, viz. Rutin, Nicotiflorin, Isoquercitrin, and Hyperoside. These compounds showed substantial docking energy (−7.9 to −11.01 kcal/mol) and intermolecular interactions with essential residues of ZIKVpro (B:His51, B:Asp75, and B:Ser135) and ZIKVRdRp (Asp540, Ile799, and Asp665) by comparison to the reference compounds, O7N inhibitor (ZIKVpro) and Sofosbuvir inhibitor (ZIKVRdRp). Besides, long interval molecular dynamics simulation (500 ns) on the selected docked poses reveals stability of the respective docked poses contributed by intermolecular hydrogen bonds and hydrophobic interactions. The predicted complex stability was further supported by calculated end-point binding free energy using molecular mechanics generalized born surface area (MM/GBSA) method. Consequently, the identified common bioflavonoids are recommended as promising therapeutic inhibitors of ZIKVpro and ZIKVRdRp against ZIKV for further experimental assessment.
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25
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Sundar S, Piramanayagam S, Natarajan J. A review on structural genomics approach applied for drug discovery against three vector-borne viral diseases: Dengue, Chikungunya and Zika. Virus Genes 2022; 58:151-171. [PMID: 35394596 DOI: 10.1007/s11262-022-01898-5] [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: 10/18/2021] [Accepted: 03/22/2022] [Indexed: 12/22/2022]
Abstract
Structural genomics involves the advent of three-dimensional structures of the genome encoded proteins through various techniques available. Numerous structural genomics research groups have been developed across the globe and they contribute enormously to the identification of three-dimensional structures of various proteins. In this review, we have discussed the applications of the structural genomics approach towards the discovery of potential lead-like molecules against the genomic drug targets of three vector-borne diseases, namely, Dengue, Chikungunya and Zika. Currently, all these three diseases are associated with the most important global public health problems and significant economic burden in tropical countries. Structural genomics has accelerated the identification of novel drug targets and inhibitors for the treatment of these diseases. We start with the current development status of the drug targets and antiviral drugs against these three diseases and conclude by describing challenges that need to be addressed to overcome the shortcomings in the process of drug discovery.
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Affiliation(s)
- Shobana Sundar
- Computational Biology Lab, Department of Bioinformatics, Bharathiar University, Coimbatore, India
| | | | - Jeyakumar Natarajan
- Data Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, Tamil Nadu, India.
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26
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Messner K, Vuong B, Tranmer GK. The Boron Advantage: The Evolution and Diversification of Boron’s Applications in Medicinal Chemistry. Pharmaceuticals (Basel) 2022; 15:ph15030264. [PMID: 35337063 PMCID: PMC8948683 DOI: 10.3390/ph15030264] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/10/2022] [Accepted: 02/13/2022] [Indexed: 12/13/2022] Open
Abstract
In this review, the history of boron’s early use in drugs, and the history of the use of boron functional groups in medicinal chemistry applications are discussed. This includes diazaborines, boronic acids, benzoxaboroles, boron clusters, and carboranes. Furthermore, critical developments from these functional groups are highlighted along with recent developments, which exemplify potential prospects. Lastly, the application of boron in the form of a prodrug, softdrug, and as a nanocarrier are discussed to showcase boron’s emergence into new and exciting fields. Overall, we emphasize the evolution of organoboron therapeutic agents as privileged structures in medicinal chemistry and outline the impact that boron has had on drug discovery and development.
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Affiliation(s)
- Katia Messner
- Rady Faculty of Health Science, College of Pharmacy, University of Manitoba, Winnipeg, MB R3E 0T5, Canada; (K.M.); (B.V.)
| | - Billy Vuong
- Rady Faculty of Health Science, College of Pharmacy, University of Manitoba, Winnipeg, MB R3E 0T5, Canada; (K.M.); (B.V.)
| | - Geoffrey K. Tranmer
- Rady Faculty of Health Science, College of Pharmacy, University of Manitoba, Winnipeg, MB R3E 0T5, Canada; (K.M.); (B.V.)
- Department of Chemistry, Faculty of Science, University of Manitoba, Winnipeg, MB R3E 0T5, Canada
- Correspondence:
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27
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Voss S, Rademann J, Nitsche C. Peptide–Bismuth Bicycles: In Situ Access to Stable Constrained Peptides with Superior Bioactivity. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202113857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Saan Voss
- Research School of Chemistry Australian National University Canberra ACT 2601 Australia
- Department of Biology, Chemistry and Pharmacy Institute of Pharmacy, Medicinal Chemistry Freie Universität Berlin Königin-Luise-Str. 2+4 14195 Berlin Germany
| | - Jörg Rademann
- Department of Biology, Chemistry and Pharmacy Institute of Pharmacy, Medicinal Chemistry Freie Universität Berlin Königin-Luise-Str. 2+4 14195 Berlin Germany
| | - Christoph Nitsche
- Research School of Chemistry Australian National University Canberra ACT 2601 Australia
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28
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Colarusso S, Ferrigno F, Ponzi S, Pavone F, Conte I, Abate L, Beghetto E, Missineo A, Amaudrut J, Bresciani A, Paonessa G, Tomei L, Montalbetti C, Bianchi E, Toniatti C, Ontoria JM. SAR Evolution towards Potent C-terminal Carboxamide Peptide Inhibitors of Zika Virus NS2B-NS3 Protease. Bioorg Med Chem 2022; 57:116631. [DOI: 10.1016/j.bmc.2022.116631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 11/28/2022]
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29
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Wahaab A, Mustafa BE, Hameed M, Stevenson NJ, Anwar MN, Liu K, Wei J, Qiu Y, Ma Z. Potential Role of Flavivirus NS2B-NS3 Proteases in Viral Pathogenesis and Anti-flavivirus Drug Discovery Employing Animal Cells and Models: A Review. Viruses 2021; 14:44. [PMID: 35062249 PMCID: PMC8781031 DOI: 10.3390/v14010044] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 02/07/2023] Open
Abstract
Flaviviruses are known to cause a variety of diseases in humans in different parts of the world. There are very limited numbers of antivirals to combat flavivirus infection, and therefore new drug targets must be explored. The flavivirus NS2B-NS3 proteases are responsible for the cleavage of the flavivirus polyprotein, which is necessary for productive viral infection and for causing clinical infections; therefore, they are a promising drug target for devising novel drugs against different flaviviruses. This review highlights the structural details of the NS2B-NS3 proteases of different flaviviruses, and also describes potential antiviral drugs that can interfere with the viral protease activity, as determined by various studies. Moreover, optimized in vitro reaction conditions for studying the NS2B-NS3 proteases of different flaviviruses may vary and have been incorporated in this review. The increasing availability of the in silico and crystallographic/structural details of flavivirus NS2B-NS3 proteases in free and drug-bound states can pave the path for the development of promising antiflavivirus drugs to be used in clinics. However, there is a paucity of information available on using animal cells and models for studying flavivirus NS2B-NS3 proteases, as well as on the testing of the antiviral drug efficacy against NS2B-NS3 proteases. Therefore, on the basis of recent studies, an effort has also been made to propose potential cellular and animal models for the study of flavivirus NS2B-NS3 proteases for the purposes of exploring flavivirus pathogenesis and for testing the efficacy of possible drugs targets, in vitro and in vivo.
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Affiliation(s)
- Abdul Wahaab
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China; (A.W.); (M.H.); (M.N.A.); (K.L.); (J.W.)
| | - Bahar E Mustafa
- Sub Campus Toba Tek Singh, University of Agriculture, Faisalabad 36050, Pakistan;
| | - Muddassar Hameed
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China; (A.W.); (M.H.); (M.N.A.); (K.L.); (J.W.)
- Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Polytechnic Institute, State University, Fralin Life Sciences Building, 360 W Campus Blacksburg, Blacksburg, VA 24061, USA
| | - Nigel J. Stevenson
- Royal College of Surgeons in Ireland, Medical University of Bahrain, Busaiteen, Adliya 15503, Bahrain;
- Viral Immunology Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 R590 Dublin, Ireland
| | - Muhammad Naveed Anwar
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China; (A.W.); (M.H.); (M.N.A.); (K.L.); (J.W.)
| | - Ke Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China; (A.W.); (M.H.); (M.N.A.); (K.L.); (J.W.)
| | - Jianchao Wei
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China; (A.W.); (M.H.); (M.N.A.); (K.L.); (J.W.)
| | - Yafeng Qiu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China; (A.W.); (M.H.); (M.N.A.); (K.L.); (J.W.)
| | - Zhiyong Ma
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China; (A.W.); (M.H.); (M.N.A.); (K.L.); (J.W.)
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30
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Luo J, Jia X, Hu Y, Chen J, Sun T. Transition-metal-free, one-pot synthesis of benzoxaboroles from o-bromobenzaldehydes via visible-light-promoted borylation. Org Biomol Chem 2021; 19:10455-10459. [PMID: 34817493 DOI: 10.1039/d1ob01853a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A novel and simple one-pot stepwise method to synthesize benzoxaboroles was demonstrated. This step-by-step synthetic method includes photocatalytic boronization with phenothiazine as a photocatalyst and sequential water-induced reduction in the presence of bis(pinacolato)diboron. A series of o-bromobenzaldehydes were well-tolerated under the standard conditions. In addition, this method has been successfully applied in the synthesis of the anti-tuberculosis candidate drug GSK 3036656 and anti-fungal drug tavaborole.
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Affiliation(s)
- Jinghan Luo
- Key Laboratory of Structure-Based Drug Design and Discovery, Shenyang Pharmaceutical University, Ministry of Education, Shenyang 110016, P.R. China.
| | - Xingxing Jia
- Key Laboratory of Structure-Based Drug Design and Discovery, Shenyang Pharmaceutical University, Ministry of Education, Shenyang 110016, P.R. China.
| | - Yanjun Hu
- Key Laboratory of Structure-Based Drug Design and Discovery, Shenyang Pharmaceutical University, Ministry of Education, Shenyang 110016, P.R. China.
| | - Jianchao Chen
- Key Laboratory of Structure-Based Drug Design and Discovery, Shenyang Pharmaceutical University, Ministry of Education, Shenyang 110016, P.R. China.
| | - Tiemin Sun
- Key Laboratory of Structure-Based Drug Design and Discovery, Shenyang Pharmaceutical University, Ministry of Education, Shenyang 110016, P.R. China.
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31
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Nie S, Zhao J, Wu X, Yao Y, Wu F, Lin YL, Li X, Kneubehl AR, Vogt MB, Rico-Hesse R, Song Y. Synthesis, structure-activity relationship and antiviral activity of indole-containing inhibitors of Flavivirus NS2B-NS3 protease. Eur J Med Chem 2021; 225:113767. [PMID: 34450494 DOI: 10.1016/j.ejmech.2021.113767] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 08/06/2021] [Accepted: 08/07/2021] [Indexed: 11/28/2022]
Abstract
Zika virus belongs to the Flavivirus family of RNA viruses, which include other important human pathogens such as dengue and West Nile virus. There are no approved antiviral drugs for these viruses. The highly conserved NS2B-NS3 protease of Flavivirus is essential for the replication of these viruses and it is therefore a drug target. Compound screen followed by medicinal chemistry optimization yielded a novel series of 2,6-disubstituted indole compounds that are potent inhibitors of Zika virus protease (ZVpro) with IC50 values as low as 320 nM. The structure-activity relationships of these and related compounds are discussed. Enzyme kinetics studies show the inhibitor 66 most likely exhibited a non-competitive mode of inhibition. In addition, this series of ZVpro inhibitors also inhibit the NS2B-NS3 protease of dengue and West Nile virus with reduced potencies. The most potent compounds 66 and 67 strongly inhibited Zika virus replication in cells with EC68 values of 1-3 μM. These compounds are novel pharmacological leads for further drug development targeting Zika virus.
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Affiliation(s)
- Shenyou Nie
- Department of Pharmacology and Chemical Biology, USA
| | - Jidong Zhao
- Department of Pharmacology and Chemical Biology, USA
| | - Xiaowei Wu
- Department of Pharmacology and Chemical Biology, USA
| | - Yuan Yao
- Department of Pharmacology and Chemical Biology, USA
| | - Fangrui Wu
- Department of Pharmacology and Chemical Biology, USA
| | - Yi-Lun Lin
- Department of Pharmacology and Chemical Biology, USA
| | - Xin Li
- Department of Pharmacology and Chemical Biology, USA
| | | | - Megan B Vogt
- Department of Molecular Virology and Microbiology, USA; Intragrative Molecular and Biomedical Sciences Graduate Program, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
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32
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Pant S, Jena NR. Inhibition of the RNA-dependent RNA Polymerase of the SARS-CoV-2 by Short Peptide Inhibitors. Eur J Pharm Sci 2021; 167:106012. [PMID: 34543728 PMCID: PMC8445883 DOI: 10.1016/j.ejps.2021.106012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/23/2021] [Accepted: 09/15/2021] [Indexed: 01/18/2023]
Abstract
The rapid proliferation of SARS-CoV-2 in COVID-19 patients has become detrimental to their lives. However, blocking the replication cycle of SARS-CoV-2 will help in suppressing the viral loads in patients, which would ultimately help in the early recovery. To discover such drugs, molecular docking, MD-simulations, and MM/GBSA approaches have been used herein to examine the role of several short ionic peptides in inhibiting the RNA binding site of the RNA-dependent RNA polymerase (RdRp). Out of the 49 tri- and tetrapeptide inhibitors studied, 8 inhibitors were found to bind RdRp strongly as revealed by the docking studies. Among these inhibitors, the Ala1-Arg2-Lys3-Asp4 and Ala1-Lys2-Lys3-Asp4 are found to make the most stable complexes with RdRp and possess the ΔGbind of -17.41 and -14.21 kcal/mol respectively as revealed by the MD and MM/GBSA studies. Hence these peptide inhibitors would be highly potent in inhibiting the activities of RdRp. It is further found that these inhibitors can occupy the positions of the nucleotide triphosphate (NTP) insertion site, thereby inhibiting the replication of the viral genome by obstructing the synthesis of new nucleotides. Structural and energetic comparisons of these inhibitors with Remdesivir and similar nucleotide drugs show that these peptides would be more specific and hence may act as promiscuous antiviral agents against RdRp.
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Affiliation(s)
- Suyash Pant
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research Kolkata, Maniktala Main Road, 700054, Kolkata, WB, India
| | - N R Jena
- Discipline of Natural Sciences, Indian Institute of Information Technology, Design, and Manufacturing, Dumna Airport Road, Jabalpur-482005, India.
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33
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Tan Y, Wu J, Song L, Zhang M, Hipolito CJ, Wu C, Wang S, Zhang Y, Yin Y. Merging the Versatile Functionalities of Boronic Acid with Peptides. Int J Mol Sci 2021; 22:ijms222312958. [PMID: 34884766 PMCID: PMC8657650 DOI: 10.3390/ijms222312958] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 11/16/2022] Open
Abstract
Peptides inherently feature the favorable properties of being easily synthesized, water-soluble, biocompatible, and typically non-toxic. Thus, boronic acid has been widely integrated with peptides with the goal of discovering peptide ligands with novel biological activities, and this effort has led to broad applications. Taking the integration between boronic acid and peptide as a starting point, we provide an overview of the latest research advances and highlight the versatile and robust functionalities of boronic acid. In this review, we summarize the diverse applications of peptide boronic acids in medicinal chemistry and chemical biology, including the identification of covalent reversible enzyme inhibitors, recognition, and detection of glycans on proteins or cancer cell surface, delivery of siRNAs, development of pH responsive devices, and recognition of RNA or bacterial surfaces. Additionally, we discuss boronic acid-mediated peptide cyclization and peptide modifications, as well as the facile chemical synthesis of peptide boronic acids, which paved the way for developing a growing number of peptide boronic acids.
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Affiliation(s)
- Yahong Tan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China; (Y.T.); (J.W.); (L.S.); (M.Z.); (C.W.); (Y.Z.)
| | - Junjie Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China; (Y.T.); (J.W.); (L.S.); (M.Z.); (C.W.); (Y.Z.)
| | - Lulu Song
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China; (Y.T.); (J.W.); (L.S.); (M.Z.); (C.W.); (Y.Z.)
| | - Mengmeng Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China; (Y.T.); (J.W.); (L.S.); (M.Z.); (C.W.); (Y.Z.)
| | - Christopher John Hipolito
- Screening & Compound Profiling, Quantitative Biosciences, Merck & Co., Inc., Kenilworth, NJ 07033, USA;
| | - Changsheng Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China; (Y.T.); (J.W.); (L.S.); (M.Z.); (C.W.); (Y.Z.)
| | - Siyuan Wang
- Department of Medicinal Chemistry, College of Pharmacy, Shenzhen Technology University, Shenzhen 518118, China
- Correspondence: (S.W.); (Y.Y.)
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China; (Y.T.); (J.W.); (L.S.); (M.Z.); (C.W.); (Y.Z.)
| | - Yizhen Yin
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China; (Y.T.); (J.W.); (L.S.); (M.Z.); (C.W.); (Y.Z.)
- Correspondence: (S.W.); (Y.Y.)
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34
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Voss S, Rademann J, Nitsche C. Peptide-Bismuth Bicycles: In Situ Access to Stable Constrained Peptides with Superior Bioactivity. Angew Chem Int Ed Engl 2021; 61:e202113857. [PMID: 34825756 DOI: 10.1002/anie.202113857] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Indexed: 12/12/2022]
Abstract
Constrained peptides are promising next-generation therapeutics. We report here a fundamentally new strategy for the facile generation of bicyclic peptides using linear precursor peptides with three cysteine residues and a non-toxic trivalent bismuth(III) salt. Peptide-bismuth bicycles form instantaneously at physiological pH, are stable in aqueous solution for many weeks, and much more resistant to proteolysis than their linear precursors. The strategy allows the in situ generation of bicyclic ligands for biochemical screening assays. We demonstrate this for two screening campaigns targeting the proteases from Zika and West Nile viruses, revealing a new lead compound that displayed inhibition constants of 23 and 150 nM, respectively. Bicyclic peptides are up to 130 times more active and 19 times more proteolytically stable than their linear analogs without bismuth.
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Affiliation(s)
- Saan Voss
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.,Department of Biology, Chemistry and Pharmacy, Institute of Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany
| | - Jörg Rademann
- Department of Biology, Chemistry and Pharmacy, Institute of Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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Dražić T, Kühl N, Gottscheber N, Hacker CN, Klein CD. The spectrum between substrates and inhibitors: Pinpointing the binding mode of dengue protease ligands with modulated basicity and hydrophobicity. Bioorg Med Chem 2021; 48:116412. [PMID: 34592636 DOI: 10.1016/j.bmc.2021.116412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/06/2021] [Accepted: 09/09/2021] [Indexed: 10/20/2022]
Abstract
Peptides can be inhibitors and substrates of proteases. The present study describes the inhibitor- vs. substrate-like properties of peptidic ligands of dengue protease which were designed to provide insight into their binding modes. Of particular interest was the localization of the cleavable peptide bond and the placement of hydrophobic elements in the binding site. The findings provide clues for the design of covalent inhibitors in which electrophilic functional groups bind to the catalytic serine, and in addition for the development of inhibitors that are less basic than the natural substrate and therefore have an improved pharmacokinetic profile. We observed a tendency of basic elements to favor a substrate-like binding mode, whereas hydrophobic elements decrease or eliminate enzymatic cleavage. This indicates a necessity to include basic elements which closely mimic the natural substrates into covalent inhibitors, posing a challenge from the chemical and pharmacokinetic perspective. However, hydrophobic elements may offer opportunities to develop non-covalent inhibitors with a favorable ADME profile and potentially improved target-binding kinetics.
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Affiliation(s)
- Tonko Dražić
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Nikos Kühl
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Nicole Gottscheber
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Christina N Hacker
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Christian D Klein
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany.
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36
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Song S, Gao P, Sun L, Kang D, Kongsted J, Poongavanam V, Zhan P, Liu X. Recent developments in the medicinal chemistry of single boron atom-containing compounds. Acta Pharm Sin B 2021; 11:3035-3059. [PMID: 34729302 PMCID: PMC8546671 DOI: 10.1016/j.apsb.2021.01.010] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/25/2020] [Accepted: 01/05/2021] [Indexed: 12/11/2022] Open
Abstract
Various boron-containing drugs have been approved for clinical use over the past two decades, and more are currently in clinical trials. The increasing interest in boron-containing compounds is due to their unique binding properties to biological targets; for example, boron substitution can be used to modulate biological activity, pharmacokinetic properties, and drug resistance. In this perspective, we aim to comprehensively review the current status of boron compounds in drug discovery, focusing especially on progress from 2015 to December 2020. We classify these compounds into groups showing anticancer, antibacterial, antiviral, antiparasitic and other activities, and discuss the biological targets associated with each activity, as well as potential future developments.
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Key Words
- ACTs, artemisinin combination therapies
- ADCs, Acinetobacter-derived cephalosporinases
- AML, acute myeloid leukemia
- AMT, aminopterin
- BLs, β-lactamases
- BNCT, boron neutron capture therapy
- BNNPs, boron nitride nanoparticles
- BNNTs, boron nitride nanotubes
- Boron-containing compounds
- CEs, carboxylesterases
- CIA, collagen-induced arthritis
- COVID-19, coronavirus disease 2019
- ClpP, casein protease P
- Covalent inhibitors
- GSH, glutathione
- HADC1, class I histone deacetylase
- HBV, hepatitis B virus
- HCV, hepatitis C virus
- HIV, human immunodeficiency virus
- LeuRS, leucyl-tRNA synthetase
- Linker components
- MBLs, metal β-lactamases
- MDR-TB, multidrug-resistant tuberculosis
- MERS, Middle East respiratory syndrome
- MIDA, N-methyliminodiacetic acid
- MM, multiple myeloma
- MTX, methotrexate
- Mcl-1, myeloid cell leukemia 1
- Mtb, Mycobacterium tuberculosis
- NA, neuraminidase
- NS5B, non-nucleoside polymerase
- OBORT, oxaborole tRNA capture
- OPs, organophosphate
- PBA, phenylboronic acid
- PDB, Protein Data Bank
- PPI, protein–protein interaction
- Prodrug
- QM, quinone methide
- RA, rheumatoid arthritis
- ROS, reactive oxygen species
- SARS-CoV-2, syndrome coronavirus 2
- SBLs, serine β-lactamases
- SERD, selective estrogen receptor downregulator
- SHA, salicyl hydroxamic acid
- SaClpP, Staphylococcus aureus caseinolytic protease P
- TB, tuberculosis
- TTR, transthyretin
- U4CR, Ugi 4-component reaction
- cUTI, complex urinary tract infection
- dCTPase, dCTPase pyrophosphatase
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Affiliation(s)
- Shu Song
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
| | - Ping Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
| | - Lin Sun
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M. DK-5230, Denmark
| | - Vasanthanathan Poongavanam
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M. DK-5230, Denmark
- Corresponding authors. Tel./fax: +86 531 88380270.
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
- Corresponding authors. Tel./fax: +86 531 88380270.
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
- Corresponding authors. Tel./fax: +86 531 88380270.
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37
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Maus H, Barthels F, Hammerschmidt SJ, Kopp K, Millies B, Gellert A, Ruggieri A, Schirmeister T. SAR of novel benzothiazoles targeting an allosteric pocket of DENV and ZIKV NS2B/NS3 proteases. Bioorg Med Chem 2021; 47:116392. [PMID: 34509861 DOI: 10.1016/j.bmc.2021.116392] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/03/2021] [Accepted: 08/30/2021] [Indexed: 01/12/2023]
Abstract
In recent years, dengue virus (DENV) and Zika virus (ZIKV), both mosquito-borne members of the Flaviviridae family, have emerged as intercontinental health issues since their vectors have spread from their tropical origins to temperate climate zones due to climate change and increasing globalization. DENV and ZIKV are positive-sense, single-stranded RNA viruses, whose genomes consist of three structural (capsid, membrane precursor, envelope) and seven non-structural (NS) proteins, all of which are initially expressed as a single precursor polyprotein. For virus maturation, the polyprotein processing is accomplished by host proteases and the viral NS2B/NS3 protease complex, whose inhibitors have been shown to be effective antiviral agents with loss of viral pathogenicity. In this work, we elucidate new structure-activity relationships of benzo[d]thiazole-based allosteric NS2B/NS3 inhibitors. We developed a new series of Y-shaped inhibitors, which, with its larger hydrophobic contact surface, should bind to previously unaddressed regions of the allosteric NS2B/NS3 binding pocket. By scaffold-hopping, we varied the benzo[d]thiazole core and identified benzofuran as a new lead scaffold shifting the selectivity of initially ZIKV-targeting inhibitors to higher activities towards the DENV protease. In addition, we were able to increase the ligand efficiency from 0.27 to 0.41 by subsequent inhibitor truncation and identified N-(5,6-dihydroxybenzo[d]thiazol-2-yl)-4-iodobenzamide as a novel sub-micromolar NS2B/NS3 inhibitor. Utilizing cell-based assays, we could prove the antiviral activity in cellulo. Overall, we report new series of sub-micromolar allosteric DENV and ZIKV inhibitors with good efficacy profile in terms of cytotoxicity and protease inhibition selectivity.
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Affiliation(s)
- Hannah Maus
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128 Mainz, Germany
| | - Fabian Barthels
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128 Mainz, Germany
| | - Stefan Josef Hammerschmidt
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128 Mainz, Germany
| | - Katja Kopp
- Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, University of Heidelberg, Im Neuenheimer Feld 344, 69120 Heidelberg, Germany
| | - Benedikt Millies
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128 Mainz, Germany
| | - Andrea Gellert
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128 Mainz, Germany
| | - Alessia Ruggieri
- Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, University of Heidelberg, Im Neuenheimer Feld 344, 69120 Heidelberg, Germany
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128 Mainz, Germany.
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38
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Abstract
Flaviviruses such as dengue, Japanese encephalitis, West Nile, Yellow Fever and Zika virus, cause viral hemorrhagic fever and encephalitis in humans. However, antiviral therapeutics to treat or prevent flavivirus infections are not yet available. Thus, there is pressing need to develop therapeutics and vaccines that target flavivirus infections. All flaviviruses carry a positive-sense single-stranded RNA genome, which encodes ten proteins; three structural proteins form the virus shell, and seven nonstructural (NS) proteins are involved in replication of the viral genome. While all NS proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5) are part of a functional membrane-bound replication complex, enzymatic activities required for flaviviral replication reside in only two NS proteins, NS3 and NS5. NS3 functions as a protease, helicase, and triphosphatase, and NS5 as a capping enzyme, methyltransferase, and RNA-dependent RNA polymerase. In this chapter, we provide an overview of viral replication focusing on the structure and function of NS3 and NS5 replicases. We further describe strategies and examples of current efforts to identify potential flavivirus inhibitors against NS3 and NS5 enzymatic activities that can be developed as therapeutic agents to combat flavivirus infections.
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Affiliation(s)
- Ekaterina Knyazhanskaya
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, TX, United States
| | - Marc C Morais
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, TX, United States
| | - Kyung H Choi
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, TX, United States.
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39
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Voss S, Nitsche C. Targeting the protease of West Nile virus. RSC Med Chem 2021; 12:1262-1272. [PMID: 34458734 PMCID: PMC8372202 DOI: 10.1039/d1md00080b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 05/17/2021] [Indexed: 01/04/2023] Open
Abstract
West Nile virus infections can cause severe neurological symptoms. During the last 25 years, cases have been reported in Asia, North America, Africa, Europe and Australia (Kunjin). No West Nile virus vaccines or specific antiviral therapies are available to date. Various viral proteins and host-cell factors have been evaluated as potential drug targets. The viral protease NS2B-NS3 is among the most promising viral targets. It releases viral proteins from a non-functional polyprotein precursor, making it a critical factor of viral replication. Despite strong efforts, no protease inhibitors have reached clinical trials yet. Substrate-derived peptidomimetics have facilitated structural elucidations of the active protease state, while alternative compounds with increased drug-likeness have recently expanded drug discovery efforts beyond the active site.
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Affiliation(s)
- Saan Voss
- Research School of Chemistry, Australian National University Canberra ACT 2601 Australia
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University Canberra ACT 2601 Australia
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40
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Soor HS, Diaz DB, Burton KI, Yudin AK. Synthesis of Fluorinated Aminoalkylboronic Acids from Amphoteric α‐Boryl Aldehydes. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202104133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Harjeet S. Soor
- Department of Chemistry University of Toronto 80 St. George St. Toronto ON M5S 3H6 Canada
| | - Diego B. Diaz
- Department of Chemistry University of Toronto 80 St. George St. Toronto ON M5S 3H6 Canada
| | - Katherine I. Burton
- Department of Chemistry University of Toronto 80 St. George St. Toronto ON M5S 3H6 Canada
| | - Andrei K. Yudin
- Department of Chemistry University of Toronto 80 St. George St. Toronto ON M5S 3H6 Canada
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41
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Soor HS, Diaz DB, Burton KI, Yudin AK. Synthesis of Fluorinated Aminoalkylboronic Acids from Amphoteric α-Boryl Aldehydes. Angew Chem Int Ed Engl 2021; 60:16366-16371. [PMID: 33977627 DOI: 10.1002/anie.202104133] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Indexed: 02/06/2023]
Abstract
Our ongoing search for underdeveloped functional group combinations has brought to light α-fluorinated aminoalkylboronic acids, a new class of molecules featuring the B-CF linkage. These compounds can now be generated from secondary amines and α-boryl aldehydes through electrophilic fluorination of boryl enamines or enamides. Fluorinated β-aminoalkylboronic acids show no signs of degradation under ambient conditions. We present evidence for the involvement of chair-like motifs, favored over the acyclic forms by up to 1.7±0.1 kcal mol-1 in water and held together by an amine-boronate hydrogen bond. Fluorinated β-aminoalkylboronic acids are stable over a wide pH range and are characterized by a pKa of 3.4, which is the lowest of any alkylboronic acid.
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Affiliation(s)
- Harjeet S Soor
- Department of Chemistry, University of Toronto, 80 St. George St., Toronto, ON, M5S 3H6, Canada
| | - Diego B Diaz
- Department of Chemistry, University of Toronto, 80 St. George St., Toronto, ON, M5S 3H6, Canada
| | - Katherine I Burton
- Department of Chemistry, University of Toronto, 80 St. George St., Toronto, ON, M5S 3H6, Canada
| | - Andrei K Yudin
- Department of Chemistry, University of Toronto, 80 St. George St., Toronto, ON, M5S 3H6, Canada
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42
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Mirzaie S, Abdi F, GhavamiNejad A, Lu B, Wu XY. Covalent Antiviral Agents. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1322:285-312. [PMID: 34258745 DOI: 10.1007/978-981-16-0267-2_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Nowadays, many viral infections have emerged and are taking a huge toll on human lives globally. Meanwhile, viral resistance to current drugs has drastically increased. Hence, there is a pressing need to design potent broad-spectrum antiviral agents to treat a variety of viral infections and overcome viral resistance. Covalent inhibitors have the potential to achieve both goals owing to their biochemical efficiency, prolonged duration of action, and the capability to inhibit shallow, solvent-exposed substrate-binding domains. In this chapter, we review the structures, activities, and inhibition mechanisms of covalent inhibitors against severe acute respiratory syndrome coronavirus 2, dengue virus, enterovirus, hepatitis C virus, human immunodeficiency virus, and influenza viruses. We also discuss the application of in silico study in covalent inhibitor design.
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Affiliation(s)
- Sako Mirzaie
- Advanced Pharmaceutics and Drug Delivery Laboratory, Leslie L. Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada.
| | - Fatemeh Abdi
- Advanced Pharmaceutics and Drug Delivery Laboratory, Leslie L. Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Amin GhavamiNejad
- Advanced Pharmaceutics and Drug Delivery Laboratory, Leslie L. Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Brian Lu
- Advanced Pharmaceutics and Drug Delivery Laboratory, Leslie L. Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Xiao Yu Wu
- Advanced Pharmaceutics and Drug Delivery Laboratory, Leslie L. Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
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43
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Amidoxime prodrugs convert to potent cell-active multimodal inhibitors of the dengue virus protease. Eur J Med Chem 2021; 224:113695. [PMID: 34298282 DOI: 10.1016/j.ejmech.2021.113695] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/05/2021] [Accepted: 07/07/2021] [Indexed: 12/16/2022]
Abstract
The flavivirus genus of the Flaviviridae family comprises Dengue, Zika and West-Nile viruses which constitute unmet medical needs as neither appropriate antivirals nor safe vaccines are available. The dengue NS2BNS3 protease is one of the most promising validated targets for developing a dengue treatment however reported protease inhibitors suffer from toxicity and cellular inefficacy. Here we report SAR on our previously reported Zika-active carbazole scaffold, culminating prodrug compound SP-471P (EC50 1.10 μM, CC50 > 100 μM) that generates SP-471; one of the most potent, non-cytotoxic and cell-active protease inhibitors described in the dengue literature. In cell-based assays, SP-471P leads to inhibition of viral RNA replication and complete abolishment of infective viral particle production even when administered 6 h post-infection. Mechanistically, SP-471 appears to inhibit both normal intermolecular protease processes and intramolecular cleavage events at the NS2BNS3 junction, as well as at NS3 internal sites, all critical for virus replication. These render SP-471 a unique to date multimodal inhibitor of the dengue protease.
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44
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Akaberi D, Båhlström A, Chinthakindi PK, Nyman T, Sandström A, Järhult JD, Palanisamy N, Lundkvist Å, Lennerstrand J. Targeting the NS2B-NS3 protease of tick-borne encephalitis virus with pan-flaviviral protease inhibitors. Antiviral Res 2021; 190:105074. [PMID: 33872674 DOI: 10.1016/j.antiviral.2021.105074] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/07/2021] [Accepted: 03/30/2021] [Indexed: 12/20/2022]
Abstract
Tick-borne encephalitis (TBE) is a severe neurological disorder caused by tick-borne encephalitis virus (TBEV), a member of the Flavivirus genus. Currently, two vaccines are available in Europe against TBEV. However, TBE cases have been rising in Sweden for the past twenty years, and thousands of cases are reported in Europe, emphasizing the need for antiviral treatments against this virus. The NS2B-NS3 protease is essential for flaviviral life cycle and has been studied as a target for the design of inhibitors against several well-known flaviviruses, but not TBEV. In the present study, Compound 86, a known tripeptidic inhibitor of dengue (DENV), West Nile (WNV) and Zika (ZIKV) proteases, was predicted to be active against TBEV protease using a combination of in silico techniques. Further, Compound 86 was found to inhibit recombinant TBEV protease with an IC50 = 0.92 μM in the in vitro enzymatic assay. Additionally, two more peptidic analogues were synthetized and they displayed inhibitory activities against both TBEV and ZIKV proteases. In particular, Compound 104 inhibited ZIKV protease with an IC50 = 0.25 μM. These compounds represent the first reported inhibitors of TBEV protease to date and provides valuable information for the further development of TBEV as well as pan-flavivirus protease inhibitors.
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Affiliation(s)
- Dario Akaberi
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | - Amanda Båhlström
- The Beijer Laboratory, Department of Medicinal Chemistry, Drug Design and Discovery, Uppsala University, Uppsala, Sweden
| | - Praveen K Chinthakindi
- The Beijer Laboratory, Department of Medicinal Chemistry, Drug Design and Discovery, Uppsala University, Uppsala, Sweden
| | - Tomas Nyman
- Protein Science Facility, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Anja Sandström
- The Beijer Laboratory, Department of Medicinal Chemistry, Drug Design and Discovery, Uppsala University, Uppsala, Sweden
| | - Josef D Järhult
- Department of Medical Sciences, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | | | - Åke Lundkvist
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | - Johan Lennerstrand
- Department of Medical Sciences, Clinical Microbiology, Uppsala University, Uppsala, Sweden.
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45
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Kühl N, Leuthold MM, Behnam MAM, Klein CD. Beyond Basicity: Discovery of Nonbasic DENV-2 Protease Inhibitors with Potent Activity in Cell Culture. J Med Chem 2021; 64:4567-4587. [PMID: 33851839 DOI: 10.1021/acs.jmedchem.0c02042] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The viral serine protease NS2B-NS3 is one of the promising targets for drug discovery against dengue virus and other flaviviruses. The molecular recognition preferences of the protease favor basic, positively charged moieties as substrates and inhibitors, which leads to pharmacokinetic liabilities and off-target interactions with host proteases such as thrombin. We here present the results of efforts that were aimed specifically at the discovery and development of noncharged, small-molecular inhibitors of the flaviviral proteases. A key factor in the discovery of these compounds was a cellular reporter gene assay for the dengue protease, the DENV2proHeLa system. Extensive structure-activity relationship explorations resulted in novel benzamide derivatives with submicromolar activities in viral replication assays (EC50 0.24 μM), selectivity against off-target proteases, and negligible cytotoxicity. This structural class has increased drug-likeness compared to most of the previously published active-site-directed flaviviral protease inhibitors and includes promising candidates for further preclinical development.
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Affiliation(s)
- Nikos Kühl
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Mila M Leuthold
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Mira A M Behnam
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Christian D Klein
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
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46
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Nie S, Yao Y, Wu F, Wu X, Zhao J, Hua Y, Wu J, Huo T, Lin YL, Kneubehl AR, Vogt MB, Ferreon J, Rico-Hesse R, Song Y. Synthesis, Structure-Activity Relationships, and Antiviral Activity of Allosteric Inhibitors of Flavivirus NS2B-NS3 Protease. J Med Chem 2021; 64:2777-2800. [PMID: 33596380 DOI: 10.1021/acs.jmedchem.0c02070] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Flaviviruses, including Zika, dengue, and West Nile viruses, are important human pathogens. The highly conserved NS2B-NS3 protease of Flavivirus is essential for viral replication and therefore a promising drug target. Through compound screening, followed by medicinal chemistry studies, a novel series of 2,5,6-trisubstituted pyrazine compounds are found to be potent, allosteric inhibitors of Zika virus protease (ZVpro) with IC50 values as low as 130 nM. Their structure-activity relationships are discussed. The ZVpro inhibitors also inhibit homologous proteases of dengue and West Nile viruses, and their inhibitory activities are correlated. The most potent compounds 47 and 103 potently inhibited Zika virus replication in cells with EC68 values of 300-600 nM and in a mouse model of Zika infection. These compounds represent novel pharmacological leads for drug development against Flavivirus infections.
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Affiliation(s)
- Shenyou Nie
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United States
| | - Yuan Yao
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United States
| | - Fangrui Wu
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United States
| | - Xiaowei Wu
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United States
| | - Jidong Zhao
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United States
| | - Yuanda Hua
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United States
| | - Jingyu Wu
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United States
| | - Tong Huo
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United States
| | - Yi-Lun Lin
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United States
| | - Alexander R Kneubehl
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United States
| | - Megan B Vogt
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United States.,Intragrative Molecular and Biomedical Sciences Graduate Program, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United States
| | - Josephine Ferreon
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United States
| | - Rebecca Rico-Hesse
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United States
| | - Yongcheng Song
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United States
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47
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Behnam MAM. Protein structural heterogeneity: A hypothesis for the basis of proteolytic recognition by the main protease of SARS-CoV and SARS-CoV-2. Biochimie 2021; 182:177-184. [PMID: 33484784 PMCID: PMC7817518 DOI: 10.1016/j.biochi.2021.01.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 01/15/2021] [Accepted: 01/15/2021] [Indexed: 02/06/2023]
Abstract
The main protease (Mpro) of SARS-CoV and SARS-CoV-2 is a key enzyme in viral replication and a promising target for the development of antiviral therapeutics. The understanding of this protein is based on a number of observations derived from earlier x-ray structures, which mostly consider substrates or ligands as the main reason behind modulation of the active site. This lead to the concept of substrate-induced subsite cooperativity as an initial attempt to explain the dual binding specificity of this enzyme in recognizing the cleavage sequences at its N- and C-termini, which are important processing steps in obtaining the mature protease. The presented hypothesis proposes that structural heterogeneity is a property of the enzyme, independent of the presence of a substrate or ligand. Indeed, the analysis of Mpro structures of SARS-CoV and SARS-CoV-2 reveals a conformational diversity for the catalytically competent state in ligand-free structures. Variation in the binding site appears to result from flexibility at residues lining the S1 subpocket and segments incorporating methionine 49 and glutamine 189. The structural evidence introduces “structure-based recognition” as a new paradigm in substrate proteolysis by Mpro. In this concept, the binding space in subpockets of the enzyme varies in a non-cooperative manner, causing distinct conformations, which recognize and process different cleavage sites, as the N- and C-termini. Insights into the recognition basis of the protease provide explanation to the ordered processing of cleavage sites. The hypothesis expands the conformational space of the enzyme and consequently opportunities for drug development and repurposing efforts.
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Affiliation(s)
- Mira A M Behnam
- Institute of Pharmacy and Molecular Biotechnology, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany.
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48
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Vega-Valdez IR, Melvin N. R, José M. SQ, D. FGE, Marvin A. SU. Docking Simulations Exhibit Bortezomib and other Boron-containing Peptidomimetics as Potential Inhibitors of SARS-CoV-2 Main Protease. CURRENT CHEMICAL BIOLOGY 2021. [DOI: 10.2174/2212796814999201102195651] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Background::
Treatment of the COVID19 pandemic requires drug development.
Boron- containing compounds are attractive chemical agents, some
of them act as proteases inhibitors.
Objective::
The present study explores the role of boronic moieties in molecules
interacting on the binding site of the SARS-CoV-2 main protease.
Methods::
Conventional docking procedure was applied by assaying boron-free
and boron-containing compounds on the recently reported crystal structure of
SARS-CoV-2 main protease (PDB code: 6LU7). The set of 150 ligands includes
bortezomib and inhibitors of coronavirus proteases.
Results::
Most of the tested compounds share contact with key residues and pose
on the cleavage pocket. The compounds with a boron atom in their structure are
often estimated to have higher affinity than boron-free analogues.
Conclusion::
Interactions and the affinity of boron-containing peptidomimetics
strongly suggest that boron-moieties increase affinity on the main protease,
which is tested by in vitro assays. A Bis-boron-containing compound previously
tested active on SARS-virus protease and bortezomib were identified as potent ligands.
These advances may be relevant to drug designing, in addition to testing
available boron-containing drugs in patients with COVID19 infection.
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Affiliation(s)
- Iván R Vega-Valdez
- Seccion de Estudios de Posgrado e Investigacion, Escuela Superior de Medicina, Instituto Politecnico Nacional, Plan de San Luis y Diaz Miron s/n, Mexico City, 11340, Mexico
| | - Rosalez Melvin N.
- Seccion de Estudios de Posgrado e Investigacion, Escuela Superior de Medicina, Instituto Politecnico Nacional, Plan de San Luis y Diaz Miron s/n, Mexico City, 11340, Mexico
| | - Santiago-Quintana José M.
- Seccion de Estudios de Posgrado e Investigacion, Escuela Superior de Medicina, Instituto Politecnico Nacional, Plan de San Luis y Diaz Miron s/n, Mexico City, 11340, Mexico
| | - Farfán-García Eunice D.
- Seccion de Estudios de Posgrado e Investigacion, Escuela Superior de Medicina, Instituto Politecnico Nacional, Plan de San Luis y Diaz Miron s/n, Mexico City, 11340, Mexico
| | - Soriano-Ursúa Marvin A.
- Seccion de Estudios de Posgrado e Investigacion, Escuela Superior de Medicina, Instituto Politecnico Nacional, Plan de San Luis y Diaz Miron s/n, Mexico City, 11340, Mexico
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49
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Lai D, Ghosh S, Hajra A. Light-induced borylation: developments and mechanistic insights. Org Biomol Chem 2021; 19:4397-4428. [PMID: 33913460 DOI: 10.1039/d1ob00323b] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Organoboron compounds are very important derivatives because of their profound impacts on medicinal, biological as well as industrial applications. The development of several novel borylation methodologies has achieved momentous interest among synthetic chemists. In this scenario, eco-friendly light-induced borylation is progressively becoming one of the best synthetic tools in recent days to prepare organoboronic ester and acid derivatives based on green chemistry rules. In this article, we have discussed all the UV- and visible-light-induced borylation strategies developed in the last decade. Furthermore, special attention is given to the mechanisms of these borylation methodologies for better understanding of reaction insights.
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Affiliation(s)
- Dipti Lai
- Department of Chemistry, Visva-Bharati (A Central University), Santiniketan 731235, India.
| | - Sumit Ghosh
- Department of Chemistry, Visva-Bharati (A Central University), Santiniketan 731235, India.
| | - Alakananda Hajra
- Department of Chemistry, Visva-Bharati (A Central University), Santiniketan 731235, India.
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50
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Schaller D, Pach S, Bermudez M, Wolber G. Exploiting Water Dynamics for Pharmacophore Screening. Methods Mol Biol 2021; 2266:227-238. [PMID: 33759130 DOI: 10.1007/978-1-0716-1209-5_13] [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: 06/12/2023]
Abstract
Three-dimensional pharmacophore models have been proven extremely valuable in exploring novel chemical space through virtual screening. However, traditional pharmacophore-based approaches need ligand information and rely on static snapshots of highly dynamic systems. In this chapter, we describe PyRod, a novel tool to generate three-dimensional pharmacophore models based on water traces of a molecular dynamics simulation of an apo-protein.The protocol described herein was successfully applied for the discovery of novel drug-like inhibitors of West Nile virus NS2B-NS3 protease. By using this recent example, we highlight the key steps of the generation and validation of PyRod-derived pharmacophore models and their application for virtual screening.
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Affiliation(s)
- David Schaller
- Pharmaceutical and Medicinal Chemistry, Freie Universität Berlin, Berlin, Germany
| | - Szymon Pach
- Pharmaceutical and Medicinal Chemistry, Freie Universität Berlin, Berlin, Germany
| | - Marcel Bermudez
- Pharmaceutical and Medicinal Chemistry, Freie Universität Berlin, Berlin, Germany
| | - Gerhard Wolber
- Pharmaceutical and Medicinal Chemistry, Freie Universität Berlin, Berlin, Germany.
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