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Alshehri MM, Danazumi AU, Alshammari MK, Bello RO, Alghazwni MK, Alshehri AM, Alshlali OM, Umar HI. Repurposing the inhibitors of MMP-9 and SGLT-2 against ubiquitin specific protease 30 in Parkinson's disease: computational modelling studies. J Biomol Struct Dyn 2024; 42:1307-1318. [PMID: 37139557 DOI: 10.1080/07391102.2023.2208223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 03/29/2023] [Indexed: 05/05/2023]
Abstract
Ubiquitin specific protease 30 (USP30) has been attributed to mitochondrial dysfunction and impediment of mitophagy in Parkinson's disease (PD). This happens once ubiquitin that supposed to bind with deformed mitochondria at the insistence of Parkin, it's been recruited by USP30 via the distal ubiquitin binding domain. This is a challenge when PINK1 and Parkin loss their functions due to mutation. Although, there are reports on USP30s' inhibitors but no study on the repurposing of inhibitors approved against MMP-9 and SGLT-2 as potential inhibitors of USP30 in PD. Thus, the highlight therein, is to repurpose approved inhibitors of MMP-9 and SGLT-2 against USP30 in PD using extensive computational modelling framework. 3D structures of Ligands and USP30 were obtained from PubChem and protein database (PDB) servers respectively, and were subjected to molecular docking, ADMET evaluation, DFT calculation, molecular dynamics simulation (MDS) and free energy calculations. Out of the 18 drugs, 2 drugs showed good binding affinity to the distal ubiquitin binding domain, moderate pharmacokinetic properties and good stability. The findings showed canagliflozin and empagliflozin as potential inhibitors of USP30. Thus, we present these drugs as repurposing candidates for the treatment of PD. However, the findings in this current study needs to be validated experimentally.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohammed M Alshehri
- Pharmaceutical Care Department, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
| | - Ammar Usman Danazumi
- Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
- Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Mohammed Kanan Alshammari
- Department of Pharmaceutical Care, Rafha Central Hospital, Rafha, North Zone, Kingdom of Saudi Arabia
| | - Ridwan Opeyemi Bello
- Computer-Aided Therapeutic Discovery and Design Group, Federal University of Technology, Akure, Nigeria
| | | | - Ahmed Mughram Alshehri
- Pharmaceutical care Department, Security Forces Hospital - Riyadh, Riyadh, Kingdom of Saudi Arabia
| | | | - Haruna Isiyaku Umar
- Computer-Aided Therapeutic Discovery and Design Group, Federal University of Technology, Akure, Nigeria
- Department of Biochemistry, Federal University of Technology, Akure, Ondo State, Nigeria
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Aminu S, Danazumi AU, Alhafiz ZA, Gorna MW, Ibrahim MA. β-Sitosterol could serve as a dual inhibitor of Trypanosoma congolense sialidase and phospholipase A 2: in vitro kinetic analyses and molecular dynamic simulations. Mol Divers 2023; 27:1645-1660. [PMID: 36042119 DOI: 10.1007/s11030-022-10517-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/15/2022] [Indexed: 11/24/2022]
Abstract
The involvement of Trypanosoma congolense sialidase alongside phospholipase A2 has been widely accepted as the major contributing factor to anemia during African animal trypanosomiasis. The enzymes aid the parasite in scavenging sialic acid and fatty acids necessary for survival in the infected host, but there are no specific drug candidates against the two enzymes. This study investigated the inhibitory effects of β-sitosterol on the partially purified T. congolense sialidase and phospholipase A2. Purification of the enzymes using DEAE cellulose column led to fractions with highest specific activities of 8016.41 and 39.26 µmol/min/mg for sialidase and phospholipase A2, respectively. Inhibition kinetics studies showed that β-sitosterol is non-competitive and an uncompetitive inhibitor of sialidase and phospholipase A2 with inhibition binding constants of 0.368 and 0.549 µM, respectively. Molecular docking of the compound revealed binding energies of - 8.0 and - 8.6 kcal/mol against the sialidase and phospholipase A2, respectively. Furthermore, 100 ns molecular dynamics simulation using GROMACS revealed stable interaction of β-sitosterol with both enzymes. Hydrogen bond interactions between the ligand and Glu284 and Leu102 residues of the sialidase and phospholipase A2, respectively, were found to be the major stabilizing forces. In conclusion, β-sitosterol could serve as a dual inhibitor of T. congolense sialidase and phospholipase A2; hence, the compound could be exploited further in the search for newer trypanocides.
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Affiliation(s)
- Suleiman Aminu
- Department of Biochemistry, Ahmadu Bello University, Zaria, Nigeria
| | - Ammar Usman Danazumi
- Biological and Chemical Research Center, Department of Chemistry, University of Warsaw, Warsaw, Poland
- Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
| | - Zainab Aliyu Alhafiz
- Department of Biochemistry, Ahmadu Bello University, Zaria, Nigeria
- Department of Biochemistry, Federal University, Gusau, Nigeria
| | - Maria Wiktoria Gorna
- Biological and Chemical Research Center, Department of Chemistry, University of Warsaw, Warsaw, Poland
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Danazumi AU, Umar HI. You must be flexible enough to be trained, Mr. Dynamics simulator. Mol Divers 2023:10.1007/s11030-023-10689-5. [PMID: 37436658 DOI: 10.1007/s11030-023-10689-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 07/02/2023] [Indexed: 07/13/2023]
Abstract
This article highlights two major problems associated with molecular dynamics studies: poor parameterization of systems and misleading interpretation of data. To address these issues, we advocate for meticulous system parameterization and careful interpretation of statistics within the framework of the study system, with a focus on high-quality and rigorous simulations. Our letter aims to encourage the adoption of the best practices in the field.
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Affiliation(s)
- Ammar Usman Danazumi
- Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland.
- Department of Biochemistry, Ahmadu Bello University, Zaria, Nigeria.
| | - Haruna Isiyaku Umar
- Computer-Aided Therapeutic Discovery and Design Platform, Federal University of Technology, Akure, Nigeria
- Department of Biochemistry, Federal University of Technology, P. M. B. 704, Akure, Ondo, Nigeria
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Danazumi AU, Ishmam IT, Idris S, Izert MA, Balogun EO, Górna MW. Targeted protein degradation might present a novel therapeutic approach in the fight against African trypanosomiasis. Eur J Pharm Sci 2023; 186:106451. [PMID: 37088149 PMCID: PMC11032742 DOI: 10.1016/j.ejps.2023.106451] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/11/2023] [Accepted: 04/20/2023] [Indexed: 04/25/2023]
Abstract
African trypanosomiasis (AT) is a hemoparasitic disease caused by infection with African trypanosomes and it is prevalent in many sub-Saharan African countries, affecting both humans and domestic animals. The disease is transmitted mostly by haematophagous insects of the genus Glossina while taking blood meal, in the process spreading the parasites from an infected animal to an uninfected animal. The disease is fatal if untreated, and the available drugs are generally ineffective and resulting in toxicities. Therefore, it is still pertinent to explore novel methods and targets for drug discovery. Proteolysis-targeting chimeras (PROTACs) present a new strategy for development of therapeutic molecules that mimic cellular proteasomal-mediated protein degradation to target proteins involved in different disease types. PROTACs have been used to degrade proteins involved in various cancers, neurodegenerative diseases, and immune disorders with remarkable success. Here, we highlight the problems associated with the current treatments for AT, discuss the concept of PROTACs and associated targeted protein degradation (TPD) approaches, and provide some insights on the future potential for the use of these emerging technologies (PROTACs and TPD) for the development of new generation of anti-Trypanosoma drugs and the first "TrypPROTACs".
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Affiliation(s)
- Ammar Usman Danazumi
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland; Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland; Department of Biochemistry, Ahmadu Bello University, Zaria, Nigeria
| | | | - Salisu Idris
- Department of Biochemistry, Ahmadu Bello University, Zaria, Nigeria
| | - Matylda Anna Izert
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland
| | - Emmanuel Oluwadare Balogun
- Department of Biochemistry, Ahmadu Bello University, Zaria, Nigeria; African Centre of Excellence for Neglected Tropical Diseases and Forensic Biotechnology, Ahmadu Bello University, Zaria, Nigeria.
| | - Maria Wiktoria Górna
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland.
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Danazumi AU, Balogun EO. Microsecond-long simulation reveals the molecular mechanism for the dual inhibition of falcipain-2 and falcipain-3 by antimalarial lead compounds. Front Mol Biosci 2022; 9:1070080. [PMID: 36601587 PMCID: PMC9806354 DOI: 10.3389/fmolb.2022.1070080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
The latest world malaria report revealed that human deaths caused by malaria are currently on the rise and presently stood at over 627,000 per year. In addition, more than 240 million people have the infection at any given time. These figures make malaria the topmost infectious disease and reiterate the need for continuous efforts for the development of novel chemotherapies. Malaria is an infectious disease caused majorly by the protozoan intracellular parasite Plasmodium falciparum and transmitted by mosquitoes. Reports abound on the central role of falcipains (cysteine protease enzymes) in the catabolism of hemoglobin for furnishing the plasmodium cells with amino acids that they require for development and survival in the hosts. Even though falcipains (FPs) have been validated as drug target molecules for the development of new antimalarial drugs, none of its inhibitory compounds have advanced beyond the early discovery stage. Therefore, there are renewed efforts to expand the collection of falcipain inhibitors. As a result, an interesting finding reported the discovery of a quinolinyl oxamide derivative (QOD) and an indole carboxamide derivative (ICD), with each compound demonstrating good potencies against the two essential FP subtypes 2 (FP-2) and 3 (FP-3). In this study, we utilized microsecond-scale molecular dynamics simulation computational method to investigate the interactions between FP-2 and FP-3 with the quinolinyl oxamide derivative and indole carboxamide derivative. The results revealed that quinolinyl oxamide derivative and indole carboxamide derivative bound tightly at the active site of both enzymes. Interestingly, despite belonging to different chemical scaffolds, they are coordinated by almost identical amino acid residues via extensive hydrogen bond interactions in both FP-2 and FP-3. Our report provided molecular insights into the interactions between FP-2 and FP-3 with quinolinyl oxamide derivative and indole carboxamide derivative, which we hope will pave the way towards the design of more potent and druglike inhibitors of these enzymes and will pave the way for their development to new antimalarial drugs.
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Affiliation(s)
- Ammar Usman Danazumi
- Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland,Groningen Research Institute of Pharmacy, University of Groningen, Groningen, Netherlands
| | - Emmanuel Oluwadare Balogun
- Department of Biochemistry, Ahmadu Bello University, Zaria, Nigeria,Africa Centre of Excellence for Neglected Tropical Diseases and Forensic Biotechnology, Ahmadu Bello University, Zaria, Nigeria,Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, United States,Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan,*Correspondence: Emmanuel Oluwadare Balogun, ,
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Danazumi AU, Iliyasu Gital S, Idris S, BS Dibba L, Balogun EO, Górna MW. Immunoinformatic design of a putative multi-epitope vaccine candidate against Trypanosoma brucei gambiense. Comput Struct Biotechnol J 2022; 20:5574-5585. [PMID: 36284708 PMCID: PMC9576565 DOI: 10.1016/j.csbj.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 09/13/2022] [Accepted: 10/02/2022] [Indexed: 11/28/2022] Open
Abstract
Human African trypanosomiasis (HAT) is a neglected tropical disease that is caused by flagellated parasites of the genus Trypanosoma. HAT imposes a significant socio-economic burden on many countries in sub-Saharan Africa and its control is hampered by several drawbacks ranging from the ineffectiveness of drugs, complex dosing regimens, drug resistance, and lack of a vaccine. Despite more than a century of research and investigations, the development of a vaccine to tackle HAT is still challenging due to the complex biology of the pathogens. Advancements in computational modeling coupled with the availability of an unprecedented amount of omics data from different organisms have allowed the design of new generation vaccines that offer better antigenicity and safety profile. One of such new generation approaches is a multi-epitope vaccine (MEV) designed from a collection of antigenic peptides. A MEV can stimulate both cellular and humoral immune responses as well as avoiding possible allergenic reactions. Herein, we take advantage of this approach to design a MEV from conserved hypothetical plasma membrane proteins of Trypanosoma brucei gambiense, the trypanosome subspecies that is responsible for the west and central African forms of HAT. The designed MEV is 402 amino acids long (41.5 kDa). It is predicted to be antigenic, non-toxic, to assume a stable 3D conformation, and to interact with a key immune receptor. In addition, immune simulation foresaw adequate immune stimulation by the putative antigen and a lasting memory. Therefore, the designed chimeric vaccine represents a potential candidate that could be used to target HAT.
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Affiliation(s)
- Ammar Usman Danazumi
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland,Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland,Groningen Research Institute of Pharmacy, University of Groningen, the Netherlands,Corresponding authors at: Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland (A.U. Danazumi, M. W. Górna).
| | | | - Salisu Idris
- Department of Biochemistry, Ahmadu Bello University, Zaria, Nigeria,Department of Medical Laboratory Science, Kazaure School of Health Technology, Jigawa, Nigeria
| | - Lamin BS Dibba
- Africa Centre of Excellence for Neglected Tropical Diseases and Forensic Biotechnology, Ahmadu Bello University, Zaria, Nigeria,Department of Physical and Natural Sciences, School of Arts and Sciences, University of the Gambia, Brikama Campus. P.O Box 3530, Serrekunda, the Gambia
| | - Emmanuel Oluwadare Balogun
- Department of Biochemistry, Ahmadu Bello University, Zaria, Nigeria,Africa Centre of Excellence for Neglected Tropical Diseases and Forensic Biotechnology, Ahmadu Bello University, Zaria, Nigeria,Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA,Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Maria Wiktoria Górna
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland,Corresponding authors at: Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland (A.U. Danazumi, M. W. Górna).
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