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Zhang Y, Ge G, Xu X, Wu J. Ensemble-Based Virtual Screening Led to the Discovery of Novel Lead Molecules as Potential NMBAs. Molecules 2024; 29:1955. [PMID: 38731447 PMCID: PMC11085220 DOI: 10.3390/molecules29091955] [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: 03/20/2024] [Revised: 04/16/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024] Open
Abstract
Neuromuscular blocking agents (NMBAs) are routinely used during anesthesia to relax skeletal muscle. Nicotinic acetylcholine receptors (nAChRs) are ligand-gated ion channels; NMBAs can induce muscle paralysis by preventing the neurotransmitter acetylcholine (ACh) from binding to nAChRs situated on the postsynaptic membranes. Despite widespread efforts, it is still a great challenge to find new NMBAs since the introduction of cisatracurium in 1995. In this work, an effective ensemble-based virtual screening method, including molecular property filters, 3D pharmacophore model, and molecular docking, was applied to discover potential NMBAs from the ZINC15 database. The results showed that screened hit compounds had better docking scores than the reference compound d-tubocurarine. In order to further investigate the binding modes between the hit compounds and nAChRs at simulated physiological conditions, the molecular dynamics simulation was performed. Deep analysis of the simulation results revealed that ZINC257459695 can stably bind to nAChRs' active sites and interact with the key residue Asp165. The binding free energies were also calculated for the obtained hits using the MM/GBSA method. In silico ADMET calculations were performed to assess the pharmacokinetic properties of hit compounds in the human body. Overall, the identified ZINC257459695 may be a promising lead compound for developing new NMBAs as an adjunct to general anesthesia, necessitating further investigations.
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Affiliation(s)
- Yi Zhang
- School of Medicine, Nanjing University, Nanjing 210093, China
- Jiangsu Key Laboratory of Central Nervous System Drug Research and Development, Jiangsu Nhwa Pharmaceutical Co., Ltd., Xuzhou 221116, China
| | - Gonghui Ge
- School of Pharmacy, China Medical University, Shenyang 110122, China
| | - Xiangyang Xu
- Jiangsu Key Laboratory of Central Nervous System Drug Research and Development, Jiangsu Nhwa Pharmaceutical Co., Ltd., Xuzhou 221116, China
| | - Jinhui Wu
- School of Medicine, Nanjing University, Nanjing 210093, China
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2
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Fedorowicz J, Sączewski J. Advances in the Synthesis of Biologically Active Quaternary Ammonium Compounds. Int J Mol Sci 2024; 25:4649. [PMID: 38731869 PMCID: PMC11083083 DOI: 10.3390/ijms25094649] [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: 04/14/2024] [Accepted: 04/19/2024] [Indexed: 05/13/2024] Open
Abstract
This review provides a comprehensive overview of recent advancements in the design and synthesis of biologically active quaternary ammonium compounds (QACs). The covered scope extends beyond commonly reviewed antimicrobial derivatives to include synthetic agents with antifungal, anticancer, and antiviral properties. Additionally, this review highlights examples of quaternary ammonium compounds exhibiting activity against protozoa and herbicidal effects, as well as analgesic and anesthetic derivatives. The article also embraces the quaternary-ammonium-containing cholinesterase inhibitors and muscle relaxants. QACs, marked by their inherent permanent charge, also find widespread usage across diverse domains such as fabric softeners, hair conditioners, detergents, and disinfectants. The effectiveness of QACs hinges greatly on finding the right equilibrium between hydrophilicity and lipophilicity. The ideal length of the alkyl chain varies according to the unique structure of each QAC and its biological settings. It is expected that this review will provide comprehensive data for medicinal and industrial chemists to design and develop novel QAC-based products.
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Affiliation(s)
- Joanna Fedorowicz
- Department of Chemical Technology of Drugs, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland
| | - Jarosław Sączewski
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland;
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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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4
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Carboranes in drug discovery, chemical biology and molecular imaging. Nat Rev Chem 2022; 6:486-504. [PMID: 37117309 DOI: 10.1038/s41570-022-00400-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2022] [Indexed: 11/08/2022]
Abstract
There exists a paucity of structural innovation and limited molecular diversity associated with molecular frameworks in drug discovery and biomolecular imaging/chemical probe design. The discovery and exploitation of new molecular entities for medical and biological applications will necessarily involve voyaging into previously unexplored regions of chemical space. Boron clusters, notably the carboranes, offer an alternative to conventional (poly)cyclic organic frameworks that may address some of the limitations associated with the use of novel molecular frameworks in chemical biology or medicine. The high thermal stability, unique 3D structure and aromaticity, kinetic inertness to metabolism and ability to engage in unusual types of intermolecular interactions, such as dihydrogen bonds, with biological receptors make carboranes exquisite frameworks in the design of probes for chemical biology, novel drug candidates and biomolecular imaging agents. This Review highlights the key developments of carborane derivatives made over the last decade as new design tools in medicinal chemistry and chemical biology, showcasing the versatility of this unique family of boron compounds.
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Kugler M, Nekvinda J, Holub J, El Anwar S, Das V, Šícha V, Pospíšilová K, Fábry M, Král V, Brynda J, Kašička V, Hajdúch M, Řezáčová P, Grüner B. Inhibitors of CA IX Enzyme Based on Polyhedral Boron Compounds. Chembiochem 2021; 22:2741-2761. [PMID: 33939874 DOI: 10.1002/cbic.202100121] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/30/2021] [Indexed: 11/12/2022]
Abstract
This review describes recent progress in the design and development of inhibitors of human carbonic anhydrase IX (CA IX) based on space-filling carborane and cobalt bis(dicarbollide) clusters. CA IX enzyme is known to play a crucial role in cancer cell proliferation and metastases. The new class of potent and selective CA IX inhibitors combines the structural motif of a bulky inorganic cluster with an alkylsulfamido or alkylsulfonamido anchor group for Zn2+ ion in the enzyme active site. Detailed structure-activity relationship (SAR) studies of a large series containing 50 compounds uncovered structural features of the cluster-containing inhibitors that are important for efficient and selective inhibition of CA IX activity. Preclinical evaluation of selected compounds revealed low toxicity, favorable pharmacokinetics and ability to reduce tumor growth. Cluster-containing inhibitors of CA IX can thus be considered as promising candidates for drug development and/or for combination therapy in boron neutron capture therapy (BNCT).
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Affiliation(s)
- Michael Kugler
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16610, Prague, Czech Republic.,Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 14220, Prague, Czech Republic
| | - Jan Nekvinda
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, Hlavní Husinec, 1001, 25068, Řež, Czech Republic
| | - Josef Holub
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, Hlavní Husinec, 1001, 25068, Řež, Czech Republic
| | - Suzan El Anwar
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, Hlavní Husinec, 1001, 25068, Řež, Czech Republic
| | - Viswanath Das
- Institute of Molecular and Translational Medicine, Hněvotínská 1333/5, 77900, Olomouc, Czech Republic
| | - Václav Šícha
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, Hlavní Husinec, 1001, 25068, Řež, Czech Republic
| | - Klára Pospíšilová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16610, Prague, Czech Republic
| | - Milan Fábry
- Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 14220, Prague, Czech Republic
| | - Vlastimil Král
- Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 14220, Prague, Czech Republic
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16610, Prague, Czech Republic.,Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 14220, Prague, Czech Republic
| | - Václav Kašička
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16610, Prague, Czech Republic
| | - Marián Hajdúch
- Institute of Molecular and Translational Medicine, Hněvotínská 1333/5, 77900, Olomouc, Czech Republic
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16610, Prague, Czech Republic.,Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 14220, Prague, Czech Republic
| | - Bohumír Grüner
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, Hlavní Husinec, 1001, 25068, Řež, Czech Republic
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Nekvinda J, Kugler M, Holub J, El Anwar S, Brynda J, Pospíšilová K, Růžičková Z, Řezáčová P, Grüner B. Direct Introduction of an Alkylsulfonamido Group on C‐sites of Isomeric Dicarba‐
closo
‐dodecaboranes: The Influence of Stereochemistry on Inhibitory Activity against the Cancer‐Associated Carbonic Anhydrase IX Isoenzyme. Chemistry 2020; 26:16541-16553. [DOI: 10.1002/chem.202002809] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/28/2020] [Indexed: 12/30/2022]
Affiliation(s)
- Jan Nekvinda
- Department of Synthesis Institute of Inorganic Chemistry of, the Czech Academy of Sciences 25068 Řež Czech Republic
| | - Michael Kugler
- Institute of Molecular Genetics Czech Academy of Sciences Vídeňská 1083 14220 Prague 4 Czech Republic
- Institute of Organic Chemistry and Biochemistry Czech Academy of, Sciences Flemingovo nám. 2 16610 Prague Czech Republic
| | - Josef Holub
- Department of Synthesis Institute of Inorganic Chemistry of, the Czech Academy of Sciences 25068 Řež Czech Republic
| | - Suzan El Anwar
- Department of Synthesis Institute of Inorganic Chemistry of, the Czech Academy of Sciences 25068 Řež Czech Republic
| | - Jiří Brynda
- Institute of Molecular Genetics Czech Academy of Sciences Vídeňská 1083 14220 Prague 4 Czech Republic
- Institute of Organic Chemistry and Biochemistry Czech Academy of, Sciences Flemingovo nám. 2 16610 Prague Czech Republic
| | - Klára Pospíšilová
- Institute of Organic Chemistry and Biochemistry Czech Academy of, Sciences Flemingovo nám. 2 16610 Prague Czech Republic
| | - Zdeňka Růžičková
- Department of General and Inorganic Chemistry Faculty of Chemical Technology University of Pardubice Studentská 573 53210 Pardubice Czech Republic
| | - Pavlína Řezáčová
- Institute of Molecular Genetics Czech Academy of Sciences Vídeňská 1083 14220 Prague 4 Czech Republic
- Institute of Organic Chemistry and Biochemistry Czech Academy of, Sciences Flemingovo nám. 2 16610 Prague Czech Republic
| | - Bohumír Grüner
- Department of Synthesis Institute of Inorganic Chemistry of, the Czech Academy of Sciences 25068 Řež Czech Republic
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