1
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Lockwood TD. Coordination chemistry suggests that independently observed benefits of metformin and Zn 2+ against COVID-19 are not independent. Biometals 2024; 37:983-1022. [PMID: 38578560 PMCID: PMC11255062 DOI: 10.1007/s10534-024-00590-5] [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: 11/24/2023] [Accepted: 02/12/2024] [Indexed: 04/06/2024]
Abstract
Independent trials indicate that either oral Zn2+ or metformin can separately improve COVID-19 outcomes by approximately 40%. Coordination chemistry predicts a mechanistic relationship and therapeutic synergy. Zn2+ deficit is a known risk factor for both COVID-19 and non-infectious inflammation. Most dietary Zn2+ is not absorbed. Metformin is a naked ligand that presumably increases intestinal Zn2+ bioavailability and active absorption by cation transporters known to transport metformin. Intracellular Zn2+ provides a natural buffer of many protease reactions; the variable "set point" is determined by Zn2+ regulation or availability. A Zn2+-interactive protease network is suggested here. The two viral cysteine proteases are therapeutic targets against COVID-19. Viral and many host proteases are submaximally inhibited by exchangeable cell Zn2+. Inhibition of cysteine proteases can improve COVID-19 outcomes and non-infectious inflammation. Metformin reportedly enhances the natural moderating effect of Zn2+ on bioassayed proteome degradation. Firstly, the dissociable metformin-Zn2+ complex could be actively transported by intestinal cation transporters; thereby creating artificial pathways of absorption and increased body Zn2+ content. Secondly, metformin Zn2+ coordination can create a non-natural protease inhibitor independent of cell Zn2+ content. Moderation of peptidolytic reactions by either or both mechanisms could slow (a) viral multiplication (b) viral invasion and (c) the pathogenic host inflammatory response. These combined actions could allow development of acquired immunity to clear the infection before life-threatening inflammation. Nirmatrelvir (Paxlovid®) opposes COVID-19 by selective inhibition the viral main protease by a Zn2+-independent mechanism. Pending safety evaluation, predictable synergistic benefits of metformin and Zn2+, and perhaps metformin/Zn2+/Paxlovid® co-administration should be investigated.
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Affiliation(s)
- Thomas D Lockwood
- Department Pharmacology and Toxicology, School of Medicine, Wright State University, Dayton, OH, 45435, USA.
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2
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D’Amato A, Mariconda A, Iacopetta D, Ceramella J, Catalano A, Sinicropi MS, Longo P. Complexes of Ruthenium(II) as Promising Dual-Active Agents against Cancer and Viral Infections. Pharmaceuticals (Basel) 2023; 16:1729. [PMID: 38139855 PMCID: PMC10747139 DOI: 10.3390/ph16121729] [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: 11/23/2023] [Revised: 12/13/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
Poor responses to medical care and the failure of pharmacological treatment for many high-frequency diseases, such as cancer and viral infections, have been widely documented. In this context, numerous metal-based substances, including cisplatin, auranofin, various gold metallodrugs, and ruthenium complexes, are under study as possible anticancer and antiviral agents. The two Ru(III) and Ru(II) complexes, namely, BOLD-100 and RAPTA-C, are presently being studied in a clinical trial and preclinical studies evaluation, respectively, as anticancer agents. Interestingly, BOLD-100 has also recently demonstrated antiviral activity against SARS-CoV-2, which is the virus responsible for the COVID-19 pandemic. Over the last years, much effort has been dedicated to discovering new dual anticancer-antiviral agents. Ru-based complexes could be very suitable in this respect. Thus, this review focuses on the most recent studies regarding newly synthesized Ru(II) complexes for use as anticancer and/or antiviral agents.
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Affiliation(s)
- Assunta D’Amato
- Department of Chemistry and Biology, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy; (A.D.); (P.L.)
| | | | - Domenico Iacopetta
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy; (D.I.); (J.C.); (M.S.S.)
| | - Jessica Ceramella
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy; (D.I.); (J.C.); (M.S.S.)
| | - Alessia Catalano
- Department of Pharmacy-Drug Sciences, University of Bari “Aldo Moro”, 70126 Bari, Italy
| | - Maria Stefania Sinicropi
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy; (D.I.); (J.C.); (M.S.S.)
| | - Pasquale Longo
- Department of Chemistry and Biology, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy; (A.D.); (P.L.)
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3
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Kumar S, Choudhary M. Design and molecular docking studies of {N 1-[2-(amino)ethyl]ethane-1,2-diamine}-[tris(oxido)]-molybdenum(VI) complex as a potential antivirus drug: from synthesis to structure. J COORD CHEM 2023. [DOI: 10.1080/00958972.2023.2173589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Sunil Kumar
- Department of Chemistry, National Institute of Technology Patna, Patna, Bihar, India
| | - Mukesh Choudhary
- Department of Chemistry, National Institute of Technology Patna, Patna, Bihar, India
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4
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Kumar S, Choudhary M. Structural and theoretical investigations, Hirshfeld surface analysis and anti-SARS CoV-2 of nickel (II) coordination complex. J Biomol Struct Dyn 2023; 41:402-422. [PMID: 34842499 DOI: 10.1080/07391102.2021.2006089] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A nickel(II) Schiff base complex, [Ni(L)(DMF)](1), was synthesized by treating NiCl2.6H2O with an ONS-donor Schiff base ligand(H2L) derived from the condensation 3,5-Dichlorosalicylaldehyde and 4,4-Dimethyl-3-thiosemicarbazide in DMF. The geometry around the center metal ion in [Ni(L)(DMF)](1) was square planar as revealed by the data collection from diffraction studies. DFT calculations were performed on the complex to get a structure-property relationship. Hirshfeld surface analysis was also carried out in the crystal structure of nickel (II) Schiff base complex. Additionally, inspiring from recent developments to find a potential inhibitor for SARS-CoV-2 virus, we have also performed molecular docking study of [Ni(L)(DMF)](1) to see if our novel complex show affinity for main protease (Mpro) of SARS-CoV-2 Mpro (PDB ID: 6LZE). Interestingly, the results are found quite encouraging where the binding affinity and inhibition constant was found to be -6.6 kcal/mol and 2.358 µM, respectively, for the best docked confirmation of complex [Ni(L)(DMF)](1) with Mpro protein. This binding affinity is reasonably well as compared to recently known antiviral drugs. For instance, the binding affinity of complex [Ni(L)(DMF)](1) is found to be better than that of recently docking results of anti-SARS-CoV-2 drugs like chloroquine (-6.293 kcal/mol), hydroxychloroquine (-5.573 kcal/mol) and remdesivir (-6.352 kcal/mol) when targeted to the active-site of SARS-CoV-2 Mpro. Besides this, molecular docking against G25K GTP-nucleotide binding protein (PDB ID: 1A4R) was also studied. We believe that current results can intrigue not only for the biomedical community but also for the materials chemists who are engaged to explore the application coordination complexes. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sunil Kumar
- Department of Chemistry, National Institute of Technology Patna, Patna, Bihar, India
| | - Mukesh Choudhary
- Department of Chemistry, National Institute of Technology Patna, Patna, Bihar, India
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5
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Rana G, Kar A, Kundal S, Musib D, Jana U. DDQ/Fe(NO 3) 3-Catalyzed Aerobic Synthesis of 3-Acyl Indoles and an In Silico Study for the Binding Affinity of N-Tosyl-3-acyl Indoles toward RdRp against SARS-CoV-2. J Org Chem 2023; 88:838-851. [PMID: 36622749 DOI: 10.1021/acs.joc.2c02009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
In the present study, we herein report a DDQ-catalyzed new protocol for the synthesis of substituted 3-acylindoles. Being a potential system for virtual hydrogen storage, introduction of catalytic DDQ in combination with Fe(NO3)3·9H2O and molecular oxygen as co-catalysts offers a regioselective oxo-functionalization of C-3 alkyl-/aryllidine indolines even with scale-up investigations. Intermediate isolation, their spectroscopic characterization, and the density functional theory calculations indicate that the method involves dehydrogenative allylic hydroxylation and 1,3-functional group isomerization/aromatization followed by terminal oxidation to afford 3-acylindoles quantitatively with very high regioselectivity. This method is very general for a large number of substrates with varieties of functional groups tolerance emerging high-yield outcome. Moreover, molecular docking studies were performed for some selected ligands with an RNA-dependent RNA polymerase complex (RdRp complex) of SARS-CoV-2 to illustrate the binding potential of those ligands. The docking results revealed that few of the ligands possess the potential to inhibit the RdRp of SARS-Cov-2 with binding energies (-6.7 to -8.19 kcal/mol), which are comparably higher with respect to the reported binding energies of the conventional re-purposed drugs such as Remdesivir, Ribavirin, and so forth (-4 to -7 kcal/mol).
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Affiliation(s)
- Gopal Rana
- Department of Chemistry, Jadavpur University, Kolkata 700 032, West Bengal, India
| | - Abhishek Kar
- Department of Chemistry, Jadavpur University, Kolkata 700 032, West Bengal, India
| | - Sandip Kundal
- Department of Chemistry, Jadavpur University, Kolkata 700 032, West Bengal, India
| | - Dulal Musib
- Department of Chemistry, National Institute of Technology Manipur, Langol, Imphal 795004, Manipur, India
| | - Umasish Jana
- Department of Chemistry, Jadavpur University, Kolkata 700 032, West Bengal, India
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6
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Kumar S, Choudhary M. New nickel( ii) Schiff base complexes as potential tools against SARS-CoV-2 Omicron target proteins: an in silico approach. NEW J CHEM 2023. [DOI: 10.1039/d2nj05136b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Herein, we report the in silico design and synthesis of two new nickel(ii) coordination complexes, based on Schiff bases derived from the 2-hydroxy-1-naphthaldehyde moiety.
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Affiliation(s)
- Sunil Kumar
- Department of Chemistry, National Institute of Technology Patna, Patna-800005, Bihar, India
| | - Mukesh Choudhary
- Department of Chemistry, National Institute of Technology Patna, Patna-800005, Bihar, India
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7
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Sharfalddin AA, Inas Muta'eb Alyounis E, Emwas AH, Jaremko M. Biological efficacy of novel metal complexes of Nitazoxanide: Synthesis, characterization, anti-COVID-19, antioxidant, antibacterial and anticancer activity studies. J Mol Liq 2022; 368:120808. [PMID: 36411838 PMCID: PMC9670593 DOI: 10.1016/j.molliq.2022.120808] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 09/24/2022] [Accepted: 11/12/2022] [Indexed: 11/18/2022]
Abstract
It has been repeatedly reported that nitazoxanide (NTZ) exhibits a wide range of antiviral activities against various viral infections and has shown antimicrobial properties against anaerobic bacteria, helminths and protozoa. To improve these properties, three novel metal complexes were synthesized. The bidentate characteristic of the NTZ ligand was characterized by different spectroscopic techniques, including Fourier transform infrared (FT-IR), thermogravimetric, nuclear magnetic resonance (NMR) and UV - visible spectroscopy. The geometries of the formed compounds were evaluated by density functional theory, and the results revealed that NTZ-Ru(III) has an octahedral geometry, while NTZ-Au(III) and NTZ-Ag(I) complexes have distorted square planar structures. Binding between the metal complexes and calf thymus DNA (Ct-DNA) has been studied via absorption spectra. Moreover, human albumen serum (HAS) titration has been carried out to test their susceptibility to interact with a major target molecule via absorption and fluorescence spectroscopic techniques. Several in vitro bioassays were performed to evaluate the biological activity, antibacterial potency against E. coli, antioxidant activity and cytotoxicity of the ligand and the obtained complexes. The results showed that complexes Ru(III) and Au(III) have the highest radical scavenging percentage while the Ag(I) demonstrated the greatest antibacterial activity. Moreover, the metal complexes presented potentially effective against E. coli. Furthermore, compared with NTZ-Ag and the free ligand, the in vitro cytotoxicity assay showed that both NTZ-Ru(III) and NTZ-Au(III) exhibited significant anticancer activity against HeLa cells. The efficiency of the novel compounds as antivirals was tested by molecular docking with two COVID-19 receptors to obtain all interaction details.
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Affiliation(s)
- Abeer A Sharfalddin
- Department of Chemistry, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | | | - Abdul-Hamid Emwas
- King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Mariusz Jaremko
- Smart-Health Initiative (SHI) and Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Jeddah, Saudi Arabia
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8
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Noor A, Qayyum S, Ali Z, Muhammad N. Syntheses and Structural Characterization of Divalent Metal Complexes (Co, Ni, Pd and Zn) of Sterically Hindered Thiourea Ligand and A Theoretical Insight of their Interaction with SARS-CoV-2 Enzyme. J Mol Struct 2022; 1274:134442. [PMID: 36337589 PMCID: PMC9621400 DOI: 10.1016/j.molstruc.2022.134442] [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: 08/25/2022] [Revised: 10/14/2022] [Accepted: 10/27/2022] [Indexed: 11/08/2022]
Abstract
Reacting two equivalents of sterically hindered 1,3-bis(2,6-diethylphenyl)thiourea ligand (L) with CoCl2, NiBr2, PdX2 (X = Cl; Br) and ZnI2 in acetonitrile afforded the corresponding bulky thiourea ligand stabilized four coordinated monomeric [L2CoCl2] (1), [L2NiBr2] (2), [L2PdX2] (3a: X = Cl; 3b: X = Br) and [L2ZnI2] (4.2CH3CN) complexes. Compound 1, 2 and 4.2CH3CN are tetrahedral whereas Pd complexes (3a and 3b) are square planar. In solution, palladium complexes are dominated by cis-isomers. Structural characterization shows inter- and intramolecular hydrogen bonding. Hirshfeld surface and fingerprint plots indicated significant intermolecular interactions in the crystal network. Molecular docking analysis revealed relatively higher SARS-CoV-2 enzyme interacting abilities of the synthesized complexes compared to the free ligand. All compounds have been characterized by elemental analyses, NMR spectroscopy and single-crystal X-ray diffraction.
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Affiliation(s)
- Awal Noor
- Department of Basic Sciences, Preparatory Year Deanship, King Faisal University, 31982 Al-Hassa, Saudi Arabia,Corresponding Author:
| | - Sadaf Qayyum
- Department of Basic Sciences, Preparatory Year Deanship, King Faisal University, 31982 Al-Hassa, Saudi Arabia
| | - Zafar Ali
- Department of Chemistry, Abdul Wali Khan University, Mardan, KPK, Pakistan
| | - Niaz Muhammad
- Department of Chemistry, Abdul Wali Khan University, Mardan, KPK, Pakistan
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9
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Synthesis and characterization of violurate - based Mn(II) and Cu(II) complexes nano-crystallites as DNA-binders and therapeutics agents against SARS-CoV-2 virus. JOURNAL OF SAUDI CHEMICAL SOCIETY 2022. [PMCID: PMC9354444 DOI: 10.1016/j.jscs.2022.101528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Synthesis and structural characterization of nano crystallites of bis-violurate-based manganese(II) and copper(II) chelates is the subject of the present study. Analytical data and mass spectra as well as thermal analysis determined the molecular formulas of the present metal chelates. Spectroscopic and magnetic measurements assigned the structural formula of the present violurate metal complexes. The spectroscopic and magnetic investigations along with structural analysis results indicated the square planar geometry of both the Mn(II) and Cu(II) complexes. The structural analysis of the synthesized metal complexes was achieved by processing the PXRD data using specialized software Expo 2014. Spectrophotometeric and viscosity measurements showed that violuric acid and its Mn(II) and Cu(II) complexes successfully bind to DNA with intrinsic binding constants Kb from 38.2 × 105 to 26.4 × 106 M−1. The antiviral activity study displayed that the inhibitory concentrations (IC50) of SARS-CoV-2 by violuric acid and its Mn(II) and Cu(II) complexes are 84.01, 39.58 and 44.86 μM respectively. Molecular docking calculations were performed on the SARS-CoV-2 virus protein and the computed binding energy values are −0.8, −3.860 −5.187 and −4.790, kcal/mol for the native ligand, violuric acid and its Mn(II) and Cu(II) complexes respectively. Insights into the relationship between structures of the current compounds and their degree of reactivity are discussed.
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10
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Mohammed Hashim KK, Manoj E, Prathapachandra Kurup MR. Bis(thio)carbohydrazone Luminogens with AIEE and ACQ Features and Their In Silico Investigations with SARS-CoV-2. ChemistrySelect 2022; 7:e202201229. [PMID: 35942361 PMCID: PMC9349619 DOI: 10.1002/slct.202201229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 07/07/2022] [Indexed: 01/09/2023]
Abstract
Herein, we report two novel multidentate luminogen proligands bis(3,5-diiodosalicylidene) carbohydrazone (H4L1) and bis(3,5-diiodosalicylidene) thiocarbohydrazone (H4L2), which are suitable candidates for biomedical applications. Though the thiocarbohydrazone H4L2 shows aggregation caused quenching (ACQ), the carbohydrazone H4L1 exhibits stronger fluorescence due to aggregation induced emission enhancement (AIEE). Molecular docking studies of H4L1 and H4L2 along with four similar (thio)carbohydrazones with the active sites of SARS-CoV-2 main protease 3CLpro reveals that the thiocarbohydrazones, in general, are showing better propensity compared to their oxygen analogues. Both the thiocarbohydrazones and the carbohydrazones, however, exhibit better binding potential at the active sites than that of some of the repurposed drugs such as chloroquine, hydroxychloroquine, lopinavir, ritonavir, darunavir and remdesivir. Also, the carbohydrazone H4L1 can be a better bioprobe compared to H4L2 as the former is found to have better binding potential with SARS-CoV-2 spike glycoprotein along with AIEE feature.
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Affiliation(s)
- K. K. Mohammed Hashim
- Department of Applied ChemistryCochin University of Science and TechnologyKochi, Kerala682 022India
| | - E. Manoj
- Department of Applied ChemistryCochin University of Science and TechnologyKochi, Kerala682 022India
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11
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Abate C, Carnamucio F, Giuffrè O, Foti C. Metal-Based Compounds in Antiviral Therapy. Biomolecules 2022; 12:933. [PMID: 35883489 PMCID: PMC9312833 DOI: 10.3390/biom12070933] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 06/29/2022] [Accepted: 07/02/2022] [Indexed: 11/16/2022] Open
Abstract
In recent years, the study of metal complexes and metal-based nanomaterials has aroused particular interest, leading to the promotion of new effective systems for the abatement of various viral diseases. Starting from the analysis of chemical properties, this review focuses on the employment of metal-based nanoparticles as antiviral drugs and how this interaction leads to a substantial enhancement in antiviral activity. The use of metal-based antiviral drugs has also spread for the formulation of antiviral vaccines, thanks especially to the remarkable adjuvant activities of some of the metal complexes. In particular, the small size and inert nature of Au- and Ag-based nanoparticles have been exploited for the design of systems for antiviral drug delivery, leading to the development of specific and safe therapies that lead to a decrease in side effects.
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Affiliation(s)
| | | | - Ottavia Giuffrè
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres 31, 98166 Messina, Italy; (C.A.); (F.C.); (C.F.)
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12
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Development of Metal Complexes for Treatment of Coronaviruses. Int J Mol Sci 2022; 23:ijms23126418. [PMID: 35742870 PMCID: PMC9223400 DOI: 10.3390/ijms23126418] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 05/29/2022] [Accepted: 06/07/2022] [Indexed: 02/04/2023] Open
Abstract
Coronavirus disease (SARS-CoV-2) is a global epidemic. This pandemic, which has been linked to high rates of death, has forced some countries throughout the world to implement complete lockdowns in order to contain the spread of infection. Because of the advent of new coronavirus variants, it is critical to find effective treatments and vaccines to prevent the virus’s rapid spread over the world. In this regard, metal complexes have attained immense interest as antibody modifiers and antiviral therapies, and they have a lot of promise towards SARS-CoV-2 and their suggested mechanisms of action are discussed, i.e., a new series of metal complexes’ medicinal vital role in treatment of specific proteins or SARS-CoV-2 are described. The structures of the obtained metal complexes were fully elucidated by different analytical and spectroscopic techniques also. Molecular docking and pharmacophore studies presented that most of complexes studied influenced good binding affinity to the main protease SARS-CoV-2, which also was attained as from the RCSB pdb (Protein Data Bank) data PDB ID: 6 W41, to expect the action of metal complexes in contradiction of COVID-19. Experimental research is required to determine the pharmacokinetics of most of the complexes analyzed for the treatment of SARS-CoV-2-related disease. Finally, the toxicity of a metal-containing inorganic complex will thus be discussed by its capability to transfer metals which may bind with targeted site.
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13
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Gorges J, Grimme S, Hansen A, Pracht P. Towards understanding solvation effects on the conformational entropy of non-rigid molecules. Phys Chem Chem Phys 2022; 24:12249-12259. [PMID: 35543018 DOI: 10.1039/d1cp05805c] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The absolute molecular entropy is a fundamental quantity for the accurate description of thermodynamic properties. For non-rigid molecules, a substantial part of the entropy can be attributed to a conformational contribution. Systems and properties where this is relevant, e.g., protein-ligand binding affinities or pKa values refer usually to the liquid phase. In this work, the influence of solvation on the conformational entropy is investigated. A recently introduced state-of-the-art and automated computational protocol for the computation of conformational entropies [Pracht et al., Chem. Sci., 2021, 12, 6551-6568.] is applied in combination with fast and accurate semiempirical quantum-chemical methods and implicit solvation models for a set of 25 commercially available drug molecules and five transition metal compounds. Computed gas-phase conformational entropies are compared with values obtained in implicit n-hexane and water. It is found that implicit solvation can have a substantial effect of several cal mol-1 K-1 on the entropy as a result of large conformational changes in the different phases. We conclude that for flexible molecules chemical accuracy for free energies in solution can only be achieved if solvation effects on the conformational ensemble are considered.
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Affiliation(s)
- Johannes Gorges
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany.
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany.
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany.
| | - Philipp Pracht
- Institute for Physical Chemistry, RWTH Aachen University, Melatener Str. 20, 52056 Aachen, Germany.
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14
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Kumar S, Choudhary M. Copper(II) Schiff base complex derived from salen ligand: structural investigation, Hirshfeld surface analysis, anticancer and anti-SARS-CoV-2. J Biomol Struct Dyn 2022:1-24. [DOI: 10.1080/07391102.2022.2076155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Sunil Kumar
- Department of Chemistry, National Institute of Technology Patna, Patna, Bihar, India
| | - Mukesh Choudhary
- Department of Chemistry, National Institute of Technology Patna, Patna, Bihar, India
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15
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Viola, Muhammad N, Khan IN, Ali Z, Ibrahim M, Shujah S, Ali S, Ikram M, Rehman S, Khan GS, Wadood A, Noor A, Schulzke C. Synthesis, characterization, antioxidant, antileishmanial, anticancer, DNA and theoretical SARS-CoV-2 interaction studies of copper(II) carboxylate complexes. J Mol Struct 2022; 1253:132308. [PMID: 34980930 PMCID: PMC8716173 DOI: 10.1016/j.molstruc.2021.132308] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 12/10/2021] [Accepted: 12/28/2021] [Indexed: 12/16/2022]
Abstract
Copper(II) carboxylate complexes [Cu2(OOCR)4L2] (1) and [Cu2(OOCR`)4OCO(R`)CuL2]n (2), where L = 2-methyl pyridine, R = 2-chlorophenyl acetate and R` = 2-fluorophenyl acetate were synthesized and characterized by FT-IR spectroscopy and single crystal X-ray analysis. Complex 1 exhibits the typical paddlewheel array of a dinuclear copper(II) complex with carboxylate ligands. In complex 2, this scaffold is further extended into a polymeric arrangement based on alternate paddlewheel and square planar moieties with distinct coordination spheres. The complexes showed better 2,2-diphenyl-1-picrylhydrazyl (DPPH) and hydroxyl radical scavenging activities and have been found to be more potent antileishmanial agents than their corresponding free ligand acid species. UV-Vis absorption titrations revealed good DNA binding abilities {Kb = 9.8 × 104 M-1 (1) and 9.9 × 104 M-1 (2)} implying partial intercalation of the complexes into DNA base pairs along with groove binding. The complexes displayed in vitro cytotoxic activity against malignant glioma U-87 (MG U87) cell lines. Computational docking studies further support complex-DNA binding by intercalation. Molecular docking investigations revealed probable interactions of the complexes with spike protein, the nucleocapsid protein of SARS-CoV-2 and with the angiotensin converting enzyme of human cells.
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Affiliation(s)
- Viola
- Department of Chemistry, Abdul Wali Khan University, Mardan, Pakistan
| | - Niaz Muhammad
- Department of Chemistry, Abdul Wali Khan University, Mardan, Pakistan,Corresponding author
| | - Ishaq N. Khan
- Institute of Basic Medical Sciences Khyber Medical University, Peshawar 25100, Pakistan
| | - Zafar Ali
- Department of Chemistry, Abdul Wali Khan University, Mardan, Pakistan
| | - Mohammad Ibrahim
- Department of Chemistry, Abdul Wali Khan University, Mardan, Pakistan
| | - Shaukat Shujah
- Department of Chemistry, Kohat University of Science and Technology, Kohat, Pakistan
| | - Saqib Ali
- Department of Chemistry, Quaid-I-Azam University Islamabad, 45320, Pakistan
| | - Muhammad Ikram
- Department of Chemistry, Abdul Wali Khan University, Mardan, Pakistan
| | - Sadia Rehman
- Department of Chemistry, Abdul Wali Khan University, Mardan, Pakistan
| | - Gul Shahzada Khan
- Department of Chemistry, College of Science, University of Bahrain, Sakhir 32038, Bahrain
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University, Mardan Pakistan
| | - Awal Noor
- Department of Basic Sciences, Preparatory Year Deanship, King Faisal University, Al-Hassa 31982, Saudi Arabia
| | - Carola Schulzke
- Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Straße 4, Greifswald 17489, Germany
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16
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In silico study of potential antiviral activity of copper(II) complexes with non–steroidal anti–inflammatory drugs on various SARS–CoV–2 target proteins. J Inorg Biochem 2022; 231:111805. [PMID: 35334392 PMCID: PMC8930182 DOI: 10.1016/j.jinorgbio.2022.111805] [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: 11/16/2021] [Revised: 03/08/2022] [Accepted: 03/14/2022] [Indexed: 11/21/2022]
Abstract
In silico molecular docking studies, in vitro toxicity and in silico predictions on the biological activity profile, pharmacokinetic properties, drug–likeness, ADMET (absorption, distribution, metabolism, excretion, and toxicity) physicochemical pharmacokinetic data, and target proteins and toxicity predictions were performed on six copper(II) complexes with the non–steroidal anti–inflammatory drugs ibuprofen, loxoprofen, fenoprofen and clonixin as ligands, in order to investigate the ability of these complexes to interact with the key therapeutic target proteins of SARS–CoV–2 (Severe Acute Respiratory Syndrome Coronavirus 2) 3C–like cysteine main protease (3CLpro/Mpro), viral papain–like protease (PLpro), RNA–dependent RNA polymerase (RdRp), and non–structural proteins (Nsps) Nsp16–Nsp10 2′–O–methyltransferase complex, and their capacity to act as antiviral agents, contributing thus to understanding the role they can play in the context of coronavirus 2019 (COVID–19) pandemic. Cytotoxic activity against five human cancer and normal cell lines were also evaluated.
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17
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Synthesis, spectroscopic characterization, and thermal studies of novel Schiff base complexes: theoretical simulation studies on coronavirus (COVID-19) using molecular docking. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2022. [PMCID: PMC8351233 DOI: 10.1007/s13738-021-02359-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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18
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Potential applicability of Schiff bases and their metal complexes during COVID-19 pandemic – a review. REV INORG CHEM 2022. [DOI: 10.1515/revic-2021-0027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Abstract
The rapid growth and revolution in the area of emerging therapeutics has been able to save the life of millions of patients globally. Besides these developments, the microbes are consistently struggling for their own survival and hence becoming quite more sturdy and incurable to existing drugs. Covid-19 virus and Black Fungus are recent examples of failure of medical preparations and strength of these viruses beyond the imagination of medical practitioners. Henceforth the study has made an extensive survey of exiting literature on heterocyclic schiff bases and their transition metal complexes to look for their potential applicability as antimicrobial agents. The inherent physiognomies of the essential properties of these transition metal complexes including thermodynamic, kinetic and chelating are comparatively modifiable as per requirements. The study has found that the biological applications of these transition metal complexes are well suited to be used as antibacterial and antifungal agents.
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19
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Kumar S, Choudhary M. Structure-based design and synthesis of copper( ii) complexes as antivirus drug candidates targeting SARS CoV-2 and HIV. NEW J CHEM 2022. [DOI: 10.1039/d2nj00703g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This paper describes the structure-based design and synthesis of two novel square-planar trans-N2O2 Cu(ii) complexes [Cu(L1)2] (1) and [Cu(L2)2] (2) of 2-((Z)-(4-methoxyphenylimino)methyl)-4,6-dichlorophenol (L1H) and 2-((Z)-(2,4-dibromophenylimino)methyl)-4-bromophenol (L2H) as potential inhibitors against the main protease of the SARS-CoV-2 and HIV viruses.
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Affiliation(s)
- Sunil Kumar
- Department of Chemistry, National Institute of Technology Patna, Patna-800005, Bihar, India
| | - Mukesh Choudhary
- Department of Chemistry, National Institute of Technology Patna, Patna-800005, Bihar, India
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20
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Kumar S, Choudhary M. Synthesis and characterization of novel copper(ii) complexes as potential drug candidates against SARS-CoV-2 main protease. NEW J CHEM 2022. [DOI: 10.1039/d2nj00283c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Two novel copper(ii) Schiff base complexes, [Cu(L1)2] (1) and [Cu(L2)(CH3OH)(Cl)] (2) of [(Z)-(5-chloro-2-((3,5-dichloro-2-hydroxybenzylidene)amino)phenyl)(phenyl)methanone (L1H) and (Z)-(2((5-bromo-2-hydroxybenzylidene)amino-5-chlorophenyl)(phenyl)methanone)(L2H)], have been designed, synthesized and characterized.
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Affiliation(s)
- Sunil Kumar
- Department of Chemistry, National Institute of Technology Patna, Patna-800005 (Bihar), India
| | - Mukesh Choudhary
- Department of Chemistry, National Institute of Technology Patna, Patna-800005 (Bihar), India
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21
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Synthesis, crystal structure, computational study and anti-virus effect of mixed ligand copper (II) complex with ONS donor Schiff base and 1, 10-phenanthroline. J Mol Struct 2021; 1246:131246. [PMID: 34658419 PMCID: PMC8510892 DOI: 10.1016/j.molstruc.2021.131246] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 07/31/2021] [Accepted: 08/03/2021] [Indexed: 12/16/2022]
Abstract
This work deals with the synthesis, crystal structure, computational study and antiviral potential of mixed ligand copper(II) complex [Cu(L)(phen)](1), (where, H2L = (Z)-N'-((E)-2-hydroxy-3,5-diiodobenzylidene)-N,N-dimethylcarbamohydrazonothioic acid, phen = 1,10-phenanthroline). The Schiff base ligand (H2L) is coordinated with Cu(II) ion in O, N, S-tridentate mode. The copper complex (1) crystallized in the monoclinic system of the space group P21/c with eight molecules in the unit cell and reveals a square pyramidal geometry. Furthermore, we also perform quantum chemical calculations to get insights into the structure-property relationship and functional properties of ligand (H2L) and its copper (II) complex [Cu(L)(phen)](1). Complex [Cu(L)(phen)](1) was also virtually designed in-silico evaluation by Swiss-ADME. Additionally, inspiring by recent developments to find a potential inhibitor for the COVID-19 virus, we have also performed molecular docking study of ligand and its copper complex (1) to see if our compounds shows an affinity for the main protease (Mpro) of COVID-19 spike protein (PDB ID: 7C8U). Interestingly, the results are found quite encouraging where the binding affinity and inhibition constant were found to be -7.14 kcal/mol and 5.82 μM for ligand (H2L) and -6.18 kcal/mol and 0.76 μM for complex [Cu(L)(phen)](1) with Mpro protein. This binding affinity is reasonably well as compared to recently known antiviral drugs. For instance, the binding affinity of ligand and complex was found to be better than docking results of chloroquine (-6.293 kcal/mol), hydroxychloroquine (-5.573 kcal/mol) and remdesivir (-6.352 kcal/mol) with Mpro protein. The present study may offer the technological solutions and potential inhibition to the COVID-19 virus in the ongoing and future challenges of the global community. In the framework of synthesis and characterization of mixed ligand copper (II) complex; the major conclusions can be drawn as follow.
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22
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A novel manganese(II) bisthiocarbohydrazone complex: Crystal structures, Hirshfeld surface analysis, DFT and molecular docking study with SARS-CoV-2. J Mol Struct 2021; 1246:131125. [DOI: 10.1016/j.molstruc.2021.131125] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/08/2021] [Accepted: 07/14/2021] [Indexed: 11/22/2022]
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23
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Pal M, Musib D, Zade AJ, Chowdhury N, Roy M. Computational Studies of Selected Transition Metal Complexes as Potential Drug Candidates against the SARS-CoV-2 Virus. ChemistrySelect 2021; 6:7429-7435. [PMID: 34541296 PMCID: PMC8441708 DOI: 10.1002/slct.202101852] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 07/20/2021] [Indexed: 12/23/2022]
Abstract
The earth has witnessed the greatest global health crisis due to the outbreak of the SARS-CoV-2 virus in late 2019, resulting in the pandemic COVID-19 with 3.38 million mortality and 163 million infections across 222 nations. Therefore, there is an urgent need for an effective therapeutic option against the SARS-CoV-2 virus. Transition metal complexes with unique chemical, kinetic and thermodynamic properties have recently emerged as the viable alternative for medicinal applications. Herein, the potential application of selected antiviral transition metal-based compounds against the SARS-CoV-2 virus was explored in silico. Initially, the transition metal-based antiviral compounds (1-5) were identified based on the structural similarity of the viral proteins (proteases, reverse transcriptase, envelop glycoproteins, etc.) of HIV, HCV, or Influenza virus with the proteins (S-protein, RNA-dependent RNA polymerase, proteases, etc) of SARS-CoV-2 virus. Hence the complexes (1-5) were subjected to ADME analysis for toxicology and pharmacokinetics report and further for the molecular docking calculations, selectively with the viral proteins of the SARS-CoV-2 virus. The molecular docking studies revealed that the iron-porphyrin complex (1) and antimalarial drug, ferroquine (2) could be the potential inhibitors of Main protease (Mpro) and spike proteins respectively of SARS-CoV-2 virus. The complex 1 exhibited high binding energy of -11.74 kcal/mol with the Mpro of SARS-CoV-2. Similarly ferroquine exhibitred binding energy of -7.43 kcal/mol against spike protein of SARS-CoV-2. The complex 5 also exhibited good binding constants values of -7.67, -8.68 and -7.82 kcal/mol with the spike protein, Mpro and RNA dependent RNA polymerase (RdRp) proteins respectively. Overall, transition metal complexes could provide an alternative and viable therapeutic solution for COVID-19.
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Affiliation(s)
- Maynak Pal
- Department of ChemistryNational Institute of Technology ManipurLangol, Imphal West, Pin795004
| | - Dulal Musib
- Department of ChemistryNational Institute of Technology ManipurLangol, Imphal West, Pin795004
| | - Aniket J. Zade
- Department of ChemistryNational Institute of Technology ManipurLangol, Imphal West, Pin795004
| | - Neeta Chowdhury
- Department of ChemistryNational Institute of Technology ManipurLangol, Imphal West, Pin795004
| | - Mithun Roy
- Department of ChemistryNational Institute of Technology ManipurLangol, Imphal West, Pin795004
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24
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Maddah M, Bahramsoltani R, Yekta NH, Rahimi R, Aliabadi R, Pourfath M. Proposing high-affinity inhibitors from Glycyrrhiza glabra L. against SARS-CoV-2 infection: virtual screening and computational analysis. NEW J CHEM 2021. [DOI: 10.1039/d1nj02031e] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Licorice as a traditional medicine introduces promising antiviral phytochemicals against SARS-CoV-2.
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Affiliation(s)
- Mina Maddah
- School of Electrical and Computer Engineering, University College of Engineering, University of Tehran, Tehran, Iran
- Super Computing Institute, University of Tehran, Tehran, Iran
| | - Roodabeh Bahramsoltani
- Department of Traditional Pharmacy, School of Persian Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - Nafiseh Hoseini Yekta
- Department of Persian Medicine, Faculty of Medicine, AJA University of Medical Sciences, Tehran, Iran
| | - Roja Rahimi
- Department of Traditional Pharmacy, School of Persian Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Phytopharmacology Interest Group (PPIG), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Rasoul Aliabadi
- School of Electrical and Computer Engineering, University College of Engineering, University of Tehran, Tehran, Iran
| | - Mahdi Pourfath
- School of Electrical and Computer Engineering, University College of Engineering, University of Tehran, Tehran, Iran
- Super Computing Institute, University of Tehran, Tehran, Iran
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