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Ali M, Zhang Z, Ibrahim MAA, Soliman MES. Heat shock protein (Hsp27)-ceramide synthase (Cers1) protein-protein interactions provide a new avenue for unexplored anti-cancer mechanism and therapy. J Recept Signal Transduct Res 2024:1-13. [PMID: 39189140 DOI: 10.1080/10799893.2024.2392711] [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: 06/19/2024] [Revised: 08/05/2024] [Accepted: 08/07/2024] [Indexed: 08/28/2024]
Abstract
Hsp27 is a member of the small heat-shock proteins (sHSPs) - the known cellular line of defence against abnormal protein folding behaviors. Nevertheless, its upregulation is linked to a variety of pathological disorders, including several types of cancers. The ceramide synthases (CerS) mediate the synthesis of ceramide, a critical structural and signaling lipid. Functionally, downstream ceramide metabolites are implicated in the apoptosis process and their abnormal functionality has been linked to anticancer resistance. Studies showed that CerS1 are possibly inhibited by Hsp27 leading to biochemical anticancer effects in vitro. Nevertheless, the nature of such protein-protein interaction (PPI) has not been considerably investigated in molecular terms, hence, we present the first description of the dynamics CerS1-Hsp27 interaction landscapes using molecular dynamics simulations. Time-scale molecular dynamics simulation analysis indicated a system-wide conformational events of decreased stability, increased flexibility, reduced compactness, and decreased folding of CerS1. Analysis of binding energy showed a favorable interaction entailing 56 residues at the interface and a total stabilizing energy of -158 KJ/mol. The CerS1 catalytic domain experienced an opposite trend compared to the protein backbone. Yet, these residues adopted a highly compact conformation as per DCCM and DSSP analysis. Furthermore, conserved residues (SER 212, ASP 213, ALA 240, GLY 243, ASP 319) comprising the substrate shuttling machinery showed notable rigidity implying a restrained ceramide precursor access and assembly; hence, a possible inhibitory mechanism. Findings from this report would streamline a better molecular understanding of CerS1-Hsp27 interactions and decipher its potential avenue toward unexplored anti-cancer mechanisms and therapy.
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Affiliation(s)
- Musab Ali
- Molecular Bio-Computation and Drug Design Research Group, School of Health Sciences, University of KwaZulu Natal, Durban, South Africa
| | - Zhichao Zhang
- School of Chemistry, Dalian University of Technology, Dalian, Liaoning, China
| | - Mahmoud A A Ibrahim
- Molecular Bio-Computation and Drug Design Research Group, School of Health Sciences, University of KwaZulu Natal, Durban, South Africa
- Computational Chemistry Laboratory, Chemistry Department, Minia University, Minia, Egypt
| | - Mahmoud E S Soliman
- Molecular Bio-Computation and Drug Design Research Group, School of Health Sciences, University of KwaZulu Natal, Durban, South Africa
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Oduro-Kwateng E, Soliman ME. DON/DRP-104 as potent serine protease inhibitors implicated in SARS-CoV-2 infection: Comparative binding modes with human TMPRSS2 and novel therapeutic approach. J Cell Biochem 2024. [PMID: 38284235 DOI: 10.1002/jcb.30528] [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: 12/03/2023] [Revised: 12/31/2023] [Accepted: 01/10/2024] [Indexed: 01/30/2024]
Abstract
Human transmembrane serine protease 2 (TMPRSS2) is an important member of the type 2 transmembrane serine protease (TTSP) family with significant therapeutic markings. The search for potent TMPRSS2 inhibitors against severe acute respiratory syndrome coronavirus 2 infection with favorable tissue specificity and off-site toxicity profiles remains limited. Therefore, probing the anti-TMPRSS2 potential of enhanced drug delivery systems, such as nanotechnology and prodrug systems, has become compelling. We report the first in silico study of TMPRSS2 against a prodrug, [isopropyl(S)-2-((S)-2-acetamido-3-(1H-indol-3-yl)-propanamido)-6-diazo-5-oxo-hexanoate] also known as DRP-104 synthesized from 6-Diazo-5-oxo-l-norleucine (DON). We performed comparative studies on DON and DRP-104 against a clinically potent TMPRSS2 inhibitor, nafamostat, and a standard serine protease inhibitor, 4-(2-Aminoethyl) benzenesulfonyl fluoride (AEBSF) against TMPRSS2 and found improved TMPRSS2 inhibition through synergistic binding of the S1/S1' subdomains. Both DON and DRP-104 had better thermodynamic profiles than AEBSF and nafamostat. DON was found to confer structural stability with strong positive correlated inter-residue motions, whereas DRP-104 was found to confer kinetic stability with restricted residue displacements and reduced loop flexibility. Interestingly, the Scavenger Receptor Cysteine-Rich (SRCR) domain of TMPRSS2 may be involved in its inhibition mechanics. Two previously unidentified loops, designated X (270-275) and Y (293-296) underwent minimal and major structural transitions, respectively. In addition, residues 273-277 consistently transitioned to a turn conformation in all ligated systems, whereas unique transitions were identified for other transitioning residue groups in each TMPRSS2-inhibitor complex. Intriguingly, while both DON and DRP-104 showed similar loop transition patterns, DRP-104 preserved loop structural integrity. As evident from our systematic comparative study using experimentally/clinically validated inhibitors, DRP-104 may serve as a potent and novel TMPRSS2 inhibitor and warrants further clinical investigation.
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Affiliation(s)
- Ernest Oduro-Kwateng
- School of Health Sciences, Molecular Bio-Computation and Drug Design Research Group, Westville Campus, University of KwaZulu Natal, Durban, South Africa
| | - Mahmoud E Soliman
- School of Health Sciences, Molecular Bio-Computation and Drug Design Research Group, Westville Campus, University of KwaZulu Natal, Durban, South Africa
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Adewumi AT, Oluyemi WM, Adekunle YA, Adewumi N, Alahmdi MI, Soliman MES, Abo‐Dya NE. Propitious Indazole Compounds as β‐ketoacyl‐ACP Synthase Inhibitors and Mechanisms Unfolded for TB Cure: Integrated Rational Design and MD Simulations. ChemistrySelect 2023. [DOI: 10.1002/slct.202203877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Adeniyi T. Adewumi
- Molecular Bio-computation and Drug Design Laboratory School of Health Sciences University of KwaZulu-Natal Westville Campus Durban 4001 South Africa
- Research Laboratories for Rational Design of Drugs and Biomaterials Isiphephelo Court, Tsakane 1550 Brakpan, Johannesburg East Rand Gauteng South Africa
| | - Wande M. Oluyemi
- Research Laboratories for Rational Design of Drugs and Biomaterials Isiphephelo Court, Tsakane 1550 Brakpan, Johannesburg East Rand Gauteng South Africa
- Department of Pharmaceutical and Medicinal Chemistry College of Pharmacy Afe Babalola University Ado-Ekiti Ekiti State Nigeria
- Laboratory for Natural Products and Biodiscovery Research Pharmaceutical Chemistry Department Faculty of Pharmacy University of Ibadan Nigeria
| | - Yemi A. Adekunle
- Research Laboratories for Rational Design of Drugs and Biomaterials Isiphephelo Court, Tsakane 1550 Brakpan, Johannesburg East Rand Gauteng South Africa
- Laboratory for Natural Products and Biodiscovery Research Pharmaceutical Chemistry Department Faculty of Pharmacy University of Ibadan Nigeria
- Centre for Natural Products Discovery (CNPD) School of Pharmacy and Biomolecular Sciences Liverpool John Moores University Liverpool L3 3AF United Kingdom
| | - Nonhlanhla Adewumi
- Research Laboratories for Rational Design of Drugs and Biomaterials Isiphephelo Court, Tsakane 1550 Brakpan, Johannesburg East Rand Gauteng South Africa
- Department of Chemistry Faculty of Applied and Computer Sciences Vaal University Vanderbijl Park South Africa
- Chemical research Laboratory BetaChem Pty Ltd ERF5 Producta Road, Driemanskap, Heidelberg 1441 Gauteng South Africa
| | - Mohamed Issa Alahmdi
- Department of Chemistry Faculty of Science University of Tabuk, Tabuk, 7149 Saudi Arabia
| | - Mahmoud E. S. Soliman
- Molecular Bio-computation and Drug Design Laboratory School of Health Sciences University of KwaZulu-Natal Westville Campus Durban 4001 South Africa
| | - Nader E. Abo‐Dya
- Department of Pharmaceutical Chemistry Faculty of Pharmacy Tabuk University Tabuk 71491 Saudi Arabia
- Department of Pharmaceutical Organic Chemistry Faculty of Pharmacy Zagazig University Zagazig 44519 Egypt
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Ciccone L, Petrarolo G, Barsuglia F, Fruchart-Gaillard C, Cassar Lajeunesse E, Adewumi AT, Soliman MES, La Motta C, Orlandini E, Nencetti S. Nature-Inspired O-Benzyl Oxime-Based Derivatives as New Dual-Acting Agents Targeting Aldose Reductase and Oxidative Stress. Biomolecules 2022; 12:448. [PMID: 35327641 PMCID: PMC8946157 DOI: 10.3390/biom12030448] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/02/2022] [Accepted: 03/05/2022] [Indexed: 02/04/2023] Open
Abstract
Aldose reductase (ALR2) is the enzyme in charge of developing cellular toxicity caused by diabetic hyperglycemia, which in turn leads to the generation of reactive oxygen species triggering oxidative stress. Therefore, inhibiting ALR2 while pursuing a concomitant anti-oxidant activity through dual-acting agents is now recognized as the gold standard treatment for preventing or at least delaying the progression of diabetic complications. Herein we describe a novel series of (E)-benzaldehyde O-benzyl oximes 6a-e, 7a-e, 8a-e, and 9-11 as ALR2 inhibitors endowed with anti-oxidant properties. Inspired by the natural products, the synthesized derivatives are characterized by a different polyhydroxy substitution pattern on their benzaldehyde fragment, which proved crucial for both the enzyme inhibitory activity and the anti-oxidant capacity. Derivatives (E)-2,3,4-trihydroxybenzaldehyde O-(3-methoxybenzyl) oxime (7b) and (E)-2,3,4-trihydroxybenzaldehyde O-(4-methoxybenzyl) oxime (8b) turned out to be the most effective dual-acting products, proving to combine the best ALR2 inhibitory properties with significant anti-oxidant efficacy.
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Affiliation(s)
- Lidia Ciccone
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy; (L.C.); (G.P.); (F.B.)
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, Commissariat à l’Énergie Atomique et aux Énergies Alternatives (CEA), Institut National de Recherche pour l’Agricolture, l’Alimentation et l’Environment (INRAE), SIMoS, 91191 Gif-sur-Yvette, France; (C.F.-G.); (E.C.L.)
- Centre for Instrumentation Sharing, University of Pisa (CISUP), Lungarno Pacinotti 43, 56126 Pisa, Italy;
| | - Giovanni Petrarolo
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy; (L.C.); (G.P.); (F.B.)
| | - Francesca Barsuglia
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy; (L.C.); (G.P.); (F.B.)
| | - Carole Fruchart-Gaillard
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, Commissariat à l’Énergie Atomique et aux Énergies Alternatives (CEA), Institut National de Recherche pour l’Agricolture, l’Alimentation et l’Environment (INRAE), SIMoS, 91191 Gif-sur-Yvette, France; (C.F.-G.); (E.C.L.)
| | - Evelyne Cassar Lajeunesse
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, Commissariat à l’Énergie Atomique et aux Énergies Alternatives (CEA), Institut National de Recherche pour l’Agricolture, l’Alimentation et l’Environment (INRAE), SIMoS, 91191 Gif-sur-Yvette, France; (C.F.-G.); (E.C.L.)
| | - Adeniyi T. Adewumi
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Science, Westville Campus, University of KwaZulu-Natal, Durban 4001, South Africa; (A.T.A.); (M.E.S.S.)
| | - Mahmoud E. S. Soliman
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Science, Westville Campus, University of KwaZulu-Natal, Durban 4001, South Africa; (A.T.A.); (M.E.S.S.)
| | - Concettina La Motta
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy; (L.C.); (G.P.); (F.B.)
- Centre for Instrumentation Sharing, University of Pisa (CISUP), Lungarno Pacinotti 43, 56126 Pisa, Italy;
| | - Elisabetta Orlandini
- Centre for Instrumentation Sharing, University of Pisa (CISUP), Lungarno Pacinotti 43, 56126 Pisa, Italy;
- Department of Earth Sciences, University of Pisa, Via Santa Maria 53, 56126 Pisa, Italy
- Research Center “E. Piaggio”, University of Pisa, Largo Lucio Lazzarino 1, 56122 Pisa, Italy
| | - Susanna Nencetti
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy; (L.C.); (G.P.); (F.B.)
- Centre for Instrumentation Sharing, University of Pisa (CISUP), Lungarno Pacinotti 43, 56126 Pisa, Italy;
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Adewumi AT, Elrashedy A, Soremekun OS, Ajadi MB, Soliman MES. Weak spots inhibition in the Mycobacterium tuberculosis antigen 85C target for antitubercular drug design through selective irreversible covalent inhibitor-SER124. J Biomol Struct Dyn 2020; 40:2934-2954. [PMID: 33155529 DOI: 10.1080/07391102.2020.1844061] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Mycobacterium tuberculosis (Mtb) encoded secreted antigen 85 enzymes (Ag85A/Ag85B/Ag85C) play that critical roles in the virulence, survival and drug-resistant TB of the pathogen. Ag85 proteins are potential antitubercular drug targets because they are essential in the catalytic synthesis of trehalose moieties and mycolic acid attachment to the Mtb cell wall. Recently, experimental protocols led to the discovery of a selective covalent Ag85 inhibitor, β-isomer monocyclic enolphosphorus Cycliphostin (CyC8β) compound, which targets the Ag85 serine 124 to exhibit a promising therapeutic activity. For the first time, our study unravelled the structural features among Mtb Ag85C homologs and motions and dynamics of Ag85C when the CyC8β bound covalently and in open model conformations to the protein using bioinformatics tools and integrated Molecular dynamics simulations. Comparative Ag85C sequence analysis revealed conserved regions; 70% active site, 90% Adeniyi loop L1 and 50% loop L2, which acts as a switch between open and closed conformations. The average C-α atoms RMSD (2.05 Å) and RMSF (0.9 Å) revealed instability and high induced flexibility in the CyC8β covalent-bound compared to the apo and open model systems, which displayed more stability and lower fluctuations. DSSP showed structural transitions of α-helices to bend and loops to 310-helices in the bound systems. SASA of CyC8β covalent bound showed active site hydrophobic residues exposure to huge solvent. Therefore, these findings present the potential opportunity hotspots in Ag85C protein that would aid the structure-based design of novel chemical entities capable of resulting in potent antitubercular drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Adeniyi T Adewumi
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Ahmed Elrashedy
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Opeyemi S Soremekun
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Mary B Ajadi
- Department of Medical Biochemistry, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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