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Girgis AS, Panda SS, Kariuki BM, Bekheit MS, Barghash RF, Aboshouk DR. Indole-Based Compounds as Potential Drug Candidates for SARS-CoV-2. Molecules 2023; 28:6603. [PMID: 37764378 PMCID: PMC10537473 DOI: 10.3390/molecules28186603] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 09/07/2023] [Accepted: 09/09/2023] [Indexed: 09/29/2023] Open
Abstract
The COVID-19 pandemic has posed a significant threat to society in recent times, endangering human health, life, and economic well-being. The disease quickly spreads due to the highly infectious SARS-CoV-2 virus, which has undergone numerous mutations. Despite intense research efforts by the scientific community since its emergence in 2019, no effective therapeutics have been discovered yet. While some repurposed drugs have been used to control the global outbreak and save lives, none have proven universally effective, particularly for severely infected patients. Although the spread of the disease is generally under control, anti-SARS-CoV-2 agents are still needed to combat current and future infections. This study reviews some of the most promising repurposed drugs containing indolyl heterocycle, which is an essential scaffold of many alkaloids with diverse bio-properties in various biological fields. The study also discusses natural and synthetic indole-containing compounds with anti-SARS-CoV-2 properties and computer-aided drug design (in silico studies) for optimizing anti-SARS-CoV-2 hits/leads.
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Affiliation(s)
- Adel S. Girgis
- Department of Pesticide Chemistry, National Research Centre, Dokki, Giza 12622, Egypt; (M.S.B.); (R.F.B.); (D.R.A.)
| | - Siva S. Panda
- Department of Chemistry and Biochemistry, Augusta University, Augusta, GA 30912, USA
- Department of Biochemistry and Molecular Biology, Augusta University, Augusta, GA 30912, USA
| | - Benson M. Kariuki
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, UK; (B.M.K.)
| | - Mohamed S. Bekheit
- Department of Pesticide Chemistry, National Research Centre, Dokki, Giza 12622, Egypt; (M.S.B.); (R.F.B.); (D.R.A.)
| | - Reham F. Barghash
- Department of Pesticide Chemistry, National Research Centre, Dokki, Giza 12622, Egypt; (M.S.B.); (R.F.B.); (D.R.A.)
| | - Dalia R. Aboshouk
- Department of Pesticide Chemistry, National Research Centre, Dokki, Giza 12622, Egypt; (M.S.B.); (R.F.B.); (D.R.A.)
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Omotuyi O, Olatunji OM, Nash O, Oyinloye B, Soremekun O, Ijagbuji A, Fatumo S. Benzimidazole compound abrogates SARS-COV-2 receptor-binding domain (RBD)/ACE2 interaction In vitro. Microb Pathog 2023; 176:105994. [PMID: 36682669 PMCID: PMC9851952 DOI: 10.1016/j.micpath.2023.105994] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 01/10/2023] [Accepted: 01/13/2023] [Indexed: 01/21/2023]
Abstract
The development of clinically actionable pharmaceuticals against coronavirus disease (COVID-19); an infectious disease caused by the SARS-CoV-2 virus is very important for ending the pandemic. Coronavirus spike glycoprotein (GP)-Receptor Binding Domain (RBD) and its interaction with host receptor angiotensin converting enzyme 2 (ACE2) is one of the most structurally understood but therapeutically untapped aspect of COVID-19 pathogenesis. Binding interface based on previous x-ray structure of RBD/ACE2 were virtually screened to identify fragments with high-binding score from 12,000 chemical building blocks. The hit compound was subjected to fingerprint-based similarity search to identify compounds within the FDA-approved drug library containing the same core scaffold. Identified compounds were then re-docked into of RBD/ACE2. The best ranked compound was validated for RBD/ACE2 inhibition using commercial kit. Molecular dynamics simulation was conducted to provide further insight into the mechanism of inhibition. From the original 12000 chemical building blocks, benzimidazole (BAZ) scaffold was identified. Fingerprint-based similarity search of the FDA-approved drug library for BAZ-containing compounds identified 12 drugs with the benzimidazole-like substructure. When these compounds were re-docked into GP/ACE2 interface, the consensus docking identified bazedoxifene as the hit. In vitro RBD/ACE2 inhibition kinetics showed micromolar IC50 value (1.237 μM) in the presence of bazedoxifene. Molecular dynamics simulation of RBD/ACE2 in the presence BAZ resulted in loss of contact and specific hydrogen-bond interaction required for RBD/ACE2 stability. Taken together, these findings identified benzimidazole scaffold as a building block for developing novel RBD/ACE2 complex inhibitor and provided mechanistic basis for the use of bazedoxifene as a repurposable drug for the treatment of COVID-19 acting at RBD/ACE2 interface.
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Affiliation(s)
- Olaposi Omotuyi
- Institute for Drug Research and Development, S.E. Bogoro Center, Afe Babalola University, Ado-Ekiti, Nigeria; Department of Pharmacology and Toxicology, College of Pharmacy, Afe Babalola University, Ado-Ekiti, Nigeria; Bio-Computing & Drug Research Unit, Mols and Sims, Ado Ekiti, Ekiti State, Nigeria.
| | - Olusina M Olatunji
- Department of Pharmacology and Toxicology, College of Pharmacy, Afe Babalola University, Ado-Ekiti, Nigeria
| | - Oyekanmi Nash
- Center for Genomics Research and Innovation, National Biotechnology Development Agency, Abuja, PMB 5118, Nigeria
| | - Babatunji Oyinloye
- Institute for Drug Research and Development, S.E. Bogoro Center, Afe Babalola University, Ado-Ekiti, Nigeria; Phytomedicine, Biochemical Toxicology and Biotechnology Research Laboratories, Department of Biochemistry, College of Sciences, Afe Babalola University, PMB 5454, Ado-Ekiti, 360001, Nigeria; Biotechnology and Structural Biology (BSB) Group, Department of Biochemistry and Microbiology, University of Zululand, Kwa-Dlangezwa, 3886, South Africa
| | - Opeyemi Soremekun
- The African Computational Genomics (TACG) Research Group, MRC/UVRI, and LSHTM, Entebbe, Uganda
| | - Ayodeji Ijagbuji
- Pharmaceutics International, Inc. Hunt Valley, Maryland, United States
| | - Segun Fatumo
- The African Computational Genomics (TACG) Research Group, MRC/UVRI, and LSHTM, Entebbe, Uganda; H3Africa Bioinformatics Network (H3ABioNet) Node, Centre for Genomics Research and Innovation, NABDA/FMST, Abuja, Nigeria; Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK.
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Basoccu F, Cuccu F, Caboni P, De Luca L, Porcheddu A. Mechanochemistry Frees Thiourea Dioxide (TDO) from the 'Veils' of Solvent, Exposing All Its Reactivity. Molecules 2023; 28:molecules28052239. [PMID: 36903485 PMCID: PMC10005452 DOI: 10.3390/molecules28052239] [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: 01/31/2023] [Revised: 02/24/2023] [Accepted: 02/25/2023] [Indexed: 03/04/2023] Open
Abstract
The synthesis of nitrogen-based heterocycles has always been considered essential in developing pharmaceuticals in medicine and agriculture. This explains why various synthetic approaches have been proposed in recent decades. However performing as methods, they often imply harsh conditions or the employment of toxic solvents and dangerous reagents. Mechanochemistry is undoubtedly one of the most promising technologies currently used for reducing any possible environmental impact, addressing the worldwide interest in counteracting environmental pollution. Following this line, we propose a new mechanochemical protocol for synthesizing various heterocyclic classes by exploiting thiourea dioxide (TDO)'s reducing proprieties and electrophilic nature. Simultaneously exploiting the low cost of a component of the textile industry such as TDO and all the advantages brought by a green technique such as mechanochemistry, we plot a route towards a more sustainable and eco-friendly methodology for preparing heterocyclic moieties.
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Affiliation(s)
- Francesco Basoccu
- Department of Chemical and Geological Sciences, University of Cagliari, 09042 Monserrato, Italy
| | - Federico Cuccu
- Department of Chemical and Geological Sciences, University of Cagliari, 09042 Monserrato, Italy
| | - Pietro Caboni
- Department of Chemical and Geological Sciences, University of Cagliari, 09042 Monserrato, Italy
| | - Lidia De Luca
- Department of Chemical, Physical, Mathematical, and Natural Sciences, University of Sassari, Via Vienna 2, 07100 Sassari, Italy
| | - Andrea Porcheddu
- Department of Chemical and Geological Sciences, University of Cagliari, 09042 Monserrato, Italy
- Correspondence:
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Upadhyay R, Khalifa Z, Patel AB. Indole Fused Benzimidazole Hybrids: A Promising Combination to Fulfill Pharmacological Significance. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2140171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Rachana Upadhyay
- Department of Chemistry, Government College, Daman (Affiliated to Veer Narmad South Gujarat University, Surat), Daman, India
| | - Zebabanu Khalifa
- Department of Chemistry, Government College, Daman (Affiliated to Veer Narmad South Gujarat University, Surat), Daman, India
| | - Amit B. Patel
- Department of Chemistry, Government College, Daman (Affiliated to Veer Narmad South Gujarat University, Surat), Daman, India
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Mudi PK, Mahato RK, Verma H, Panda SJ, Purohit CS, Silakari O, Biswas B. In silico anti-SARS-CoV-2 activities of five-membered heterocycle-substituted benzimidazoles. J Mol Struct 2022; 1261:132869. [PMID: 35340531 PMCID: PMC8934690 DOI: 10.1016/j.molstruc.2022.132869] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/10/2022] [Accepted: 03/17/2022] [Indexed: 12/16/2022]
Abstract
The manuscript deals with cost-effective synthesis, structural characterization and in silico SARS-CoV-2 screening activity of 5-membered heterocycle-substituted benzimidazole derivatives, 1-((1H-pyrrol-2-yl)methyl)-2-(1H-pyrrol-2-yl)-1H-benzo[d]imidazole (L1), 2-(furan-2-yl)-1-(furan-2-ylmethyl)-1H-benzo[d]imidazole (L2), 2-(thiophen-2-yl)-1-(thiophen-2-ylmethyl)-1H-benzo[d]imidazole (L3). The benzimidazole compounds were synthesized through a green-synthetic approach by coupling of 5-membered heterocyclic-carboxaldehyde and o-phenylenediamine in water under an aerobic condition. The compounds were characterized by various spectroscopic methods and X-ray structural analysis. The suitable single-crystals of the methyl derivative of L3 were grown as L3' which crystallized in a monoclinic system and the thiophene groups co-existed in a nearly a perpendicular orientation. Further, in silico anti-SARS-CoV-2 proficiency of the synthetic derivatives is evaluated against main protease (Mpro) and non-structural proteins (nsp2 and nsp7) of SARS-CoV-2. Molecular docking and molecular dynamics analysis of the ligands (L1-L3) against Mpro and nsp2 and nsp7 for 50 ns reveal that L3 turns out to be the superlative antiviral candidate against Mpro, nsp2 and nsp7 of SARS-CoV-2 as evident from the binding score and stability of the ligand-docked complexes with considerable binding energy changes.
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Affiliation(s)
| | - Rajani Kanta Mahato
- Department of Chemistry, University of North Bengal, Darjeeling 734013, India
| | - Himanshu Verma
- Molecular Modeling Lab, Department Pharmaceutical Sciences and Drug Research, Punjabi University, India
| | - Subhra Jyoti Panda
- Department of Chemical Sciences, National School of Science Education and Research, Bhubaneswar 752050, India
| | - Chandra Sekhar Purohit
- Department of Chemical Sciences, National School of Science Education and Research, Bhubaneswar 752050, India
| | - Om Silakari
- Molecular Modeling Lab, Department Pharmaceutical Sciences and Drug Research, Punjabi University, India
| | - Bhaskar Biswas
- Department of Chemistry, University of North Bengal, Darjeeling 734013, India,Corresponding author
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