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Waqas M, Ullah S, Ullah A, Halim SA, Rehman NU, Khalid A, Ali A, Khan A, Gibbons S, Csuk R, Al-Harrasi A. Disrupting protease and deubiquitinase activities of SARS-CoV-2 papain-like protease by natural and synthetic products discovered through multiple computational and biochemical approaches. Int J Biol Macromol 2024; 277:134476. [PMID: 39111477 DOI: 10.1016/j.ijbiomac.2024.134476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 07/31/2024] [Accepted: 08/02/2024] [Indexed: 08/12/2024]
Abstract
The single-stranded RNA genome of SARS-CoV-2 encodes several structural and non-structural proteins, among which the papain-like protease (PLpro) is crucial for viral replication and immune evasion and has emerged as a promising therapeutic target. The current study aims to discover new inhibitors of PLpro that can simultaneously disrupt its protease and deubiquitinase activities. Using multiple computational approaches, six compounds (CP1-CP6) were selected from our in-house compounds database, with higher docking scores (-7.97 kcal/mol to -8.14 kcal/mol) and fitted well in the active pocket of PLpro. Furthermore, utilizing microscale molecular dynamics simulations (MD), the dynamic behavior of selected compounds was studied. Those molecules strongly binds at the PLpro active site and forms stable complexes. The dynamic motions suggest that the binding of CP1-CP6 brought the protein to a closed conformational state, thereby altering its normal function. In an in vitro evaluation, CP2 showed the most significant inhibitory potential for PLpro (protease activity = 2.71 ± 0.33 μM and deubiquitinase activity = 3.11 ± 0.75 μM), followed by CP1, CP5, CP4 and CP6. Additionally, CP1-CP6 showed no cytotoxicity at a concentration of 30 μM in the human BJ cell line.
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Affiliation(s)
- Muhammad Waqas
- Department of Biotechnology and Genetic Engineering, Hazara University, Mansehra 2100, Pakistan
| | - Saeed Ullah
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Sultanate of Oman
| | - Atta Ullah
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Sultanate of Oman
| | - Sobia Ahsan Halim
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Sultanate of Oman
| | - Najeeb Ur Rehman
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Sultanate of Oman
| | - Asaad Khalid
- Health Research Center, Jazan University, P.O. Box: 114, Jazan 45142, Saudi Arabia
| | - Amjad Ali
- Department of Biotechnology and Genetic Engineering, Hazara University, Mansehra 2100, Pakistan.
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Sultanate of Oman.
| | - Simon Gibbons
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Sultanate of Oman
| | - Rene Csuk
- Martin-Luther-University Halle-Wittenberg, Organic Chemistry, Kurt-Mothes-Str. 2, D-06120 Halle (Saale), Germany
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Sultanate of Oman.
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Jamshidi-adegani F, Vakilian S, Rehman NU, Al-Broumi M, Al-kindi J, Alam K, Mozafarinahavandi P, Hasan A, Al-Riyami H, Hussain J, White S, Al-Harrasi A, Al-Hashmi S. Secondary metabolites from acridocarpus orientalis inhibits 4T1 cells and promotes mesenchymal stem cells (MSCs) proliferation. Mol Biol Rep 2020; 47:5421-5430. [DOI: 10.1007/s11033-020-05632-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 06/26/2020] [Indexed: 12/18/2022]
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Balhamar SOMS, Panicker NG, Akhlaq S, Qureshi MM, Ahmad W, Rehman NU, Ali L, Al-Harrasi A, Hussain J, Mustafa F. Differential Cytotoxic Potential of Acridocarpus orientalis Leaf and Stem Extracts with the Ability to Induce Multiple Cell Death Pathways. Molecules 2019; 24:molecules24213976. [PMID: 31684146 PMCID: PMC6864630 DOI: 10.3390/molecules24213976] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/24/2019] [Accepted: 10/31/2019] [Indexed: 12/18/2022] Open
Abstract
This study systematically analyzed the anticancer potential of Acridocarpus orientalis (AO), a traditional medicinal plant of the Arabian Peninsula/East Africa known for its anti-inflammatory and pain relief properties. Tests of serial organic fractions from methanolic extracts of its leaves and stems revealed that only some fractions showed anti-proliferative potential with the dichloromethane fraction from leaves (AOD (L)) showing the most cytotoxic effect against both breast (MCF-7 and MDA-MB-231) and cervical (HeLa) cancer cell lines. The n-butanol fraction from the stems (AOB (S)), on the other hand, was more effective against cervical cancer cells and did not harm the normal cells. Further characterization of the mode of cell killing revealed that AOD (L) depended more on non-apoptotic pathways for its cytotoxicity in breast cancer cells, while it could activate some apoptosis and necroptosis in HeLa cells. The AOB (S) fraction could primarily activate apoptosis and some necroptosis in HeLa cells. Both fractions perturbed autophagy, but in a dissimilar manner. Thus, different parts of A. orientalis revealed variable potential to induce cell death in cancer cells via apoptotic and non-apoptotic pathways, making A. orientalis a valuable plant for the exploration of anticancer bioactive reagents, some of which may be protective for normal cells.
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Affiliation(s)
| | - Neena Gopinathan Panicker
- Department of Biochemistry, College of Medicine & Health Sciences, United Arab Emirates (UAE) University, Al Ain, P.O. Box 17666, UAE.
| | - Shaima Akhlaq
- Department of Biochemistry, College of Medicine & Health Sciences, United Arab Emirates (UAE) University, Al Ain, P.O. Box 17666, UAE.
| | - Mohammed Mansoor Qureshi
- Department of Biochemistry, College of Medicine & Health Sciences, United Arab Emirates (UAE) University, Al Ain, P.O. Box 17666, UAE.
| | - Waqar Ahmad
- Department of Biochemistry, College of Medicine & Health Sciences, United Arab Emirates (UAE) University, Al Ain, P.O. Box 17666, UAE.
| | - Najeeb Ur Rehman
- Natural and Medical Sciences Research Center, University of Nizwa, Sultanate of Oman, Nizwa, Oman.
| | - Liaqat Ali
- Natural and Medical Sciences Research Center, University of Nizwa, Sultanate of Oman, Nizwa, Oman.
- Department of Chemistry, University of Sargodha, Sub-Campus Mianwali, Punjab 42200, Pakistan.
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Sultanate of Oman, Nizwa, Oman.
| | - Javid Hussain
- Department of Biological Sciences & Chemistry, College of Arts and Sciences, University of Nizwa, Sultanate of Oman.
| | - Farah Mustafa
- Department of Biochemistry, College of Medicine & Health Sciences, United Arab Emirates (UAE) University, Al Ain, P.O. Box 17666, UAE.
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