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Nazir MS, Ahmad M, Aslam S, Rafiq A, Al-Hussain SA, Zaki MEA. A Comprehensive Update of Anti-COVID-19 Activity of Heterocyclic Compounds. Drug Des Devel Ther 2024; 18:1547-1571. [PMID: 38737333 PMCID: PMC11088867 DOI: 10.2147/dddt.s450499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/24/2024] [Indexed: 05/14/2024] Open
Abstract
The Coronavirus disease 2019 (COVID-19) pandemic is one of the most considerable health problems across the world. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the major causative agent of COVID-19. The severe symptoms of this deadly disease include shortness of breath, fever, cough, loss of smell, and a broad spectrum of other health issues such as diarrhea, pneumonia, bronchitis, septic shock, and multiple organ failure. Currently, there are no medications available for coronavirus patients, except symptom-relieving drugs. Therefore, SARS-CoV-2 requires the development of effective drugs and specific treatments. Heterocycles are important constituents of more than 85% of the physiologically active pharmaceutical drugs on the market now. Several FDA-approved drugs have been reported including molnupiravir, remdesivir, ritonavir, oseltamivir, favipiravir, chloroquine, and hydroxychloroquine for the cure of COVID-19. In this study, we discuss potent anti-SARS-CoV-2 heterocyclic compounds that have been synthesized over the past few years. These compounds included; indole, piperidine, pyrazine, pyrimidine, pyrrole, piperazine, quinazoline, oxazole, quinoline, isoxazole, thiazole, quinoxaline, pyrazole, azafluorene, imidazole, thiadiazole, triazole, coumarin, chromene, and benzodioxole. Both in vitro and in silico studies were performed to determine the potential of these heterocyclic compounds in the fight against various SARS-CoV-2 proteins.
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Affiliation(s)
| | - Matloob Ahmad
- Department of Chemistry, Government College University, Faisalabad, Pakistan
| | - Sana Aslam
- Department of Chemistry, Government College Women University, Faisalabad, Pakistan
| | - Ayesha Rafiq
- Department of Chemistry, Government College University, Faisalabad, Pakistan
| | - Sami A Al-Hussain
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Magdi E A Zaki
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
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2
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Kanzouai Y, Laghmari M, Yamari I, Bouzammit R, Bahsis L, Benali T, Chtita S, Bakhouch M, Akhazzane M, El Kouali M, Hammani K, Al Houari G. Chromone-isoxazole hybrids molecules: synthesis, spectroscopic, MEDT, ELF, antibacterial, ADME-Tox, molecular docking and MD simulation investigations. J Biomol Struct Dyn 2023:1-15. [PMID: 37817499 DOI: 10.1080/07391102.2023.2266022] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 07/01/2023] [Indexed: 10/12/2023]
Abstract
A mechanistic study was performed within the molecular electron density theory at the B3LYP/6-311G (d,p) computational level to explain the regioselectivity observed. An electron localization function analysis was also performed, and the results confirm the zwitterionic-type (zw-type) mechanism of the cycloaddition reactions between nitrile oxide and alkylated 4H-chromene-2-carboxylate derivatives and shed more light on the obtained regioselectivity experimentally. In silico studies on the pharmacokinetics, ADME and toxicity tests of the compounds were also performed, and it was projected that compounds 5a, 5b, 5c and 5d are pharmacokinetic and have favorable ADME profiles. Moreover, docking and molecular dynamics investigations were conducted to evaluate the interactions, orientation and conformation of the target compounds on the active sites of four distinct enzymes. The results of this investigation showed that two compounds, 5a and 5c, interacted effectively with the S. aureus active site while maintaining acceptable binding energy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Youssra Kanzouai
- Engineering Laboratory of Organometallic and Molecular Materials and Environment, Department of Chemistry, Faculty of Sciences Dhar El Mahraz, University of Sidi Mohamed Ben Abdellah, Fez, Morocco
| | - Mustapha Laghmari
- Laboratory of Natural Resources and Environment, Department of Biology Polydisciplinary Faculty of Taza, Sidi Mohamed Ben Abdellah University, Taza, Morocco
| | - Imane Yamari
- Laboratory of Analytical and Molecular Chemistry, Department of Chemistry, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca, Casablanca, Morocco
| | - Rachid Bouzammit
- Engineering Laboratory of Organometallic and Molecular Materials and Environment, Department of Chemistry, Faculty of Sciences Dhar El Mahraz, University of Sidi Mohamed Ben Abdellah, Fez, Morocco
| | - Lahoucine Bahsis
- Laboratoire de Chimie Analytique et Moléculaire, LCAM, Département de Chimie, Faculté Polydisciplinaire de Safi, Université Cadi Ayyad, Safi, Morocco
| | - Taoufiq Benali
- Laboratory of Natural Resources and Environment, Department of Biology Polydisciplinary Faculty of Taza, Sidi Mohamed Ben Abdellah University, Taza, Morocco
- Environment and Health Team, Polydisciplinary Faculty of Safi, Department of Biology, Cadi Ayyad University, Safi, Morocco
| | - Samir Chtita
- Laboratory of Analytical and Molecular Chemistry, Department of Chemistry, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca, Casablanca, Morocco
| | - Mohamed Bakhouch
- Bioorganic Chemistry Team, Department of Chemistry, Faculty of Sciences, University Chouaïb Doukkali, El Jadida, Morocco
| | - Mohamed Akhazzane
- Cité de l'innovation, Université Sidi Mohamed Ben Abdellah, Fez, Morocco
| | - M'hammed El Kouali
- Laboratory of Analytical and Molecular Chemistry, Department of Chemistry, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca, Casablanca, Morocco
| | - Khalil Hammani
- Laboratory of Natural Resources and Environment, Department of Biology Polydisciplinary Faculty of Taza, Sidi Mohamed Ben Abdellah University, Taza, Morocco
| | - Ghali Al Houari
- Engineering Laboratory of Organometallic and Molecular Materials and Environment, Department of Chemistry, Faculty of Sciences Dhar El Mahraz, University of Sidi Mohamed Ben Abdellah, Fez, Morocco
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Edache EI, Uzairu A, Mamza PA, Shallangwa GA, Yagin FH, Abdel Samee N, Mahmoud NF. Combining docking, molecular dynamics simulations, AD-MET pharmacokinetics properties, and MMGBSA calculations to create specialized protocols for running effective virtual screening campaigns on the autoimmune disorder and SARS-CoV-2 main protease. Front Mol Biosci 2023; 10:1254230. [PMID: 37771457 PMCID: PMC10523577 DOI: 10.3389/fmolb.2023.1254230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 08/15/2023] [Indexed: 09/30/2023] Open
Abstract
The development of novel medicines to treat autoimmune diseases and SARS-CoV-2 main protease (Mpro), a virus that can cause both acute and chronic illnesses, is an ongoing necessity for the global community. The primary objective of this research is to use CoMFA methods to evaluate the quantitative structure-activity relationship (QSAR) of a select group of chemicals concerning autoimmune illnesses. By performing a molecular docking analysis, we may verify previously observed tendencies and gain insight into how receptors and ligands interact. The results of the 3D QSAR models are quite satisfactory and give significant statistical results: Q_loo∧2 = 0.5548, Q_lto∧2 = 0.5278, R∧2 = 0.9990, F-test = 3,101.141, SDEC = 0.017 for the CoMFA FFDSEL, and Q_loo∧2 = 0.7033, Q_lto∧2 = 0.6827, Q_lmo∧2 = 0.6305, R∧2 = 0.9984, F-test = 1994.0374, SDEC = 0.0216 for CoMFA UVEPLS. The success of these two models in exceeding the external validation criteria used and adhering to the Tropsha and Glorbaikh criteria's upper and lower bounds can be noted. We report the docking simulation of the compounds as an inhibitor of the SARS-CoV-2 Mpro and an autoimmune disorder in this context. For a few chosen autoimmune disorder receptors (protein tyrosine phosphatase, nonreceptor type 22 (lymphoid) isoform 1 (PTPN22), type 1 diabetes, rheumatoid arthritis, and SARS-CoV-2 Mpro, the optimal binding characteristics of the compounds were described. According to their potential for effectiveness, the studied compounds were ranked, and those that demonstrated higher molecular docking scores than the reference drugs were suggested as potential new drug candidates for the treatment of autoimmune disease and SARS-CoV-2 Mpro. Additionally, the results of analyses of drug similarity, ADME (Absorption, Distribution, Metabolism, and Excretion), and toxicity were used to screen the best-docked compounds in which compound 4 scaled through. Finally, molecular dynamics (MD) simulation was used to verify compound 4's stability in the complex with the chosen autoimmune diseases and SARS-CoV-2 Mpro protein. This compound showed a steady trajectory and molecular characteristics with a predictable pattern of interactions. These findings suggest that compound 4 may hold potential as a therapy for autoimmune diseases and SARS-CoV-2 Mpro.
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Affiliation(s)
| | - Adamu Uzairu
- Department of Chemistry, Ahmadu Bello University, Zaria, Nigeria
| | | | | | - Fatma Hilal Yagin
- Department of Biostatistics and Medical Informatics, Faculty of Medicine, Inonu University, Malatya, Türkiye
| | - Nagwan Abdel Samee
- Department of Information Technology, College of Computer and Information Sciences, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Noha F. Mahmoud
- Rehabilitation Sciences Department, Health and Rehabilitation Sciences College, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
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Fitoz A, Yazan Z. Experimental and theoretical approaches to interactions between DNA and purine metabolism products. Int J Biol Macromol 2023; 248:125961. [PMID: 37487992 DOI: 10.1016/j.ijbiomac.2023.125961] [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: 03/15/2023] [Revised: 06/13/2023] [Accepted: 07/12/2023] [Indexed: 07/26/2023]
Abstract
Deoxyribonucleic acid (DNA) is a significant target for small organic and inorganic drug molecules. Understanding the DNA interaction mechanism of these molecules is vital for new drug designs. In this work, interactions between xanthine (XT), theophylline (TP), and theobromine (TB) with calf-thymus double-strained DNA (dsDNA) were monitored via an experimental and theoretical approach. Experimentally, cyclic voltammetry (CV) and differential pulse voltammetry (DPV) techniques were used on the surface of the NiO/MWCNT/NNaM/PGE electrochemical platform in vitro. Kinetic parameters, including diffusion coefficients, surface concentrations, and standard heterogeneous rate constants, were measured in the absence and presence of DNA using scan rate studies. In the presence of DNA, kinetic parameters were observed to be reduced significantly. Thermodynamic parameters, such as DNA binding constants and standard free Gibbs energies, were calculated for each molecule using the CV and DPV techniques. Both techniques suggested a binding affinity order of XT > TB > TP. Theoretically, density functional theory was applied for geometry optimization, natural bond orbital analyses, and molecular orbital energies of XT, TP, and TB. Experimental and theoretical binding affinities confirm each other. The most energetically stable ligand-DNA complexes expressed that XT, TP, and TB interact with dsDNA via minor groove binding mode, using mostly hydrogen bonds.
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Affiliation(s)
- Alper Fitoz
- Ankara University, Faculty of Science, Department of Chemistry, 06560, Turkey
| | - Zehra Yazan
- Ankara University, Faculty of Science, Department of Chemistry, 06560, Turkey.
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Romanov-Michailidis F, Hsiao CC, Urner LM, Jerhaoui S, Surkyn M, Miller B, Vos A, Dominguez Blanco M, Bueters R, Vinken P, Bekkers M, Walker D, Pietrak B, Eyckmans W, Dores-Sousa JL, Joo Koo S, Lento W, Bauser M, Philippar U, Rombouts FJR. Discovery of an Oral, Beyond-Rule-of-Five Mcl-1 Protein-Protein Interaction Modulator with the Potential of Treating Hematological Malignancies. J Med Chem 2023; 66:6122-6148. [PMID: 37114951 DOI: 10.1021/acs.jmedchem.2c01953] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Avoidance of apoptosis is critical for the development and sustained growth of tumors. The pro-survival protein myeloid cell leukemia 1 (Mcl-1) is an anti-apoptotic member of the Bcl-2 family of proteins which is overexpressed in many cancers. Upregulation of Mcl-1 in human cancers is associated with high tumor grade, poor survival, and resistance to chemotherapy. Therefore, pharmacological inhibition of Mcl-1 is regarded as an attractive approach to treating relapsed or refractory malignancies. Herein, we disclose the design, synthesis, optimization, and early preclinical evaluation of a potent and selective small-molecule inhibitor of Mcl-1. Our exploratory design tactics focused on structural modifications which improve the potency and physicochemical properties of the inhibitor while minimizing the risk of functional cardiotoxicity. Despite being in the "non-Lipinski" beyond-Rule-of-Five property space, the developed compound benefits from exquisite oral bioavailability in vivo and induces potent pharmacodynamic inhibition of Mcl-1 in a mouse xenograft model.
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Affiliation(s)
| | - Chien-Chi Hsiao
- Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Lorenz M Urner
- Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Soufyan Jerhaoui
- Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Michel Surkyn
- Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Bradley Miller
- Janssen Research & Development LLC, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
| | - Ann Vos
- Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | | | - Ruud Bueters
- Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Petra Vinken
- Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Mariette Bekkers
- Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - David Walker
- Janssen Research & Development LLC, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
| | - Beth Pietrak
- Janssen Research & Development LLC, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
| | - Werner Eyckmans
- Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | | | - Seong Joo Koo
- Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - William Lento
- Janssen Research & Development LLC, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
| | - Marcus Bauser
- Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Ulrike Philippar
- Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
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Pradhan S, Prasad R, Sinha C, Sen P. Molecular modeling of potent novel sulfonamide derivatives as non-peptide small molecule anti-COVID 19 agents. J Biomol Struct Dyn 2022; 40:7129-7142. [PMID: 34060418 PMCID: PMC8171005 DOI: 10.1080/07391102.2021.1897043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 02/19/2021] [Indexed: 11/26/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent for the COVID-19. The Sulfonamides groups have been widely introduced in several drugs, especially for their antibacterial activities and generally prescribed for respiratory infections. On the other hand, imidazole groups have the multipotency to act as drugs, including antiviral activity. We have used a structure-based drug design approach to design some imidazole derivatives of sulfonamide, which can efficiently bind to the active site of SARS-CoV-2 main protease and thus may have the potential to inhibit its proteases activity. We conducted molecular docking and molecular dynamics simulation to observe the stability and flexibility of inhibitor complexes. We have checked ADMET (absorption, distribution, metabolism, excretion and toxicity) and drug-likeness rules to scrutinize toxicity and then designed the most potent compound based on computational chemistry. Our small predicted molecule non-peptide protease inhibitors could provide a useful model in the further search for novel compounds since it has many advantages over peptidic drugs, like lower side effects, toxicity and less chance of drug resistance. Further, we confirmed the stability of our inhibitor-complex and interaction profile through the Molecular dynamics simulation study. Our small predicted moleculeCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sayantan Pradhan
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Kolkata, India
| | - Ramesh Prasad
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | | | - Prosenjit Sen
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Kolkata, India
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Theoretical and Experimental Studies of Hydrogen Bonded Dihydroxybenzene Isomers Polyurethane Adhesive Material. Polymers (Basel) 2022; 14:polym14091701. [PMID: 35566870 PMCID: PMC9105584 DOI: 10.3390/polym14091701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 04/18/2022] [Accepted: 04/20/2022] [Indexed: 12/04/2022] Open
Abstract
Hydrogen bonding in polyurethane (PU) is imposed by molecular parameters. In this study, the effect of structural isomerism of certain monomers on hydrogen bonding of waterborne polyurethane (WBPU) was studied theoretically and experimentally. Two dihydroxybenzene (DHB)-based structural isomers such as catechol (CC) and hydroquinone (HQ), with different OH positions on the inner benzene core, had been used. Two series of WBPU dispersions were prepared using CC and HQ with defined contents. The binding energies between the catechol (CC)/hydroquinone (HQ) (respective OH group) and urethane/urea were calculated theoretically. By using a density functional theory (DFT) method, it was found that the largest binding energy between the urea and CC was higher than that of urea and HQ. The FT-IR analysis of synthesized polymer was also carried out to compare the results with the theoretical values. The CC-based polymers showed a stronger hydrogen bond both theoretically and experimentally than those for HQ-based polymers. The higher level of hydrogen bond was reflected in their properties of CC-based polymers. The adhesive strength, thermal stability, and hydrophobicity were higher for CC-based materials than those for HQ-based materials. The adhesive strength was increased 25% with the addition of 2.0 wt% CC content. This adhesive strength slightly deviated at a moderately high temperature of 80 °C.
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Synthesis & characterization of heterocyclic disazo - azomethine dyes and investigating their molecular docking & dynamics properties on acetylcholine esterase (AChE), heat shock protein (HSP90α), nicotinamide N-methyl transferase (NNMT) and SARS-CoV-2 (2019-nCoV, COVID-19) main protease (Mpro). J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131974] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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