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Faraji N, Daly NL, Arab SS, Khosroushahi AY. In silico design of potential Mcl-1 peptide-based inhibitors. J Mol Model 2024; 30:108. [PMID: 38499818 DOI: 10.1007/s00894-024-05901-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 03/10/2024] [Indexed: 03/20/2024]
Abstract
CONTEXT BIM (Bcl-2 interacting mediator of apoptosis)-derived peptides that specifically target over-expressed Mcl-1 (myeloid cell leukemia-1) protein and induce apoptosis are potentially anti-cancer agents. Since the helicity of BIM-derived peptides has a crucial role in their functionality, a range of strategies have been used to increase the helicity including the introduction of unnatural residues and stapling methods that have some drawbacks such as the accumulation in the liver. To avoid these drawbacks, this study aimed to design a more helical peptide by utilizing bioinformatics algorithms and molecular dynamics simulations without exploiting unnatural residues and stapling methods. MM-PBSA results showed that the mutations of A4fE and A2eE in analogue 5 demonstrate a preference towards binding with Mcl-1. As evidenced by Circular dichroism results, the helicity increases from 18 to 34%, these findings could enhance the potential of analogue 5 as an anti-cancer agent targeting Mcl-1. The applied strategies in this research could shed light on the in silico peptide design. Moreover, analogue 5 as a drug candidate can be evaluated in vitro and in vivo studies. METHODS The sequence of the lead peptide was determined using the ApInAPDB database and PRALINE program. Contact finder and PDBsum web server softwares were used to determine the contact involved amino acids in complex with Mcl-1. All identified salt bridge contributing residues were unaltered to preserve the binding affinity. After proposing novel analogues, their secondary structures were predicted by Cham finder web server software and GOR, Neural Network, and Chou-Fasman algorithms. Finally, molecular dynamics simulations run for 100 ns were done using the GROMACS, version 5.0.7, with the CHARMM36 force field. MM-PBSA was used to assess binding affinity specificity in targeting Mcl-1 and Bcl-xL (B-cell lymphoma extra-large).
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Affiliation(s)
- Naser Faraji
- Department of Medical Nanotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Daneshgah Street, Tabriz, Iran
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Norelle L Daly
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, 4870, Australia
| | - Seyed Shahriar Arab
- Department of Biophysics, Faculty of Biological Sciences, School of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Ahmad Yari Khosroushahi
- Department of Medical Nanotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Daneshgah Street, Tabriz, Iran.
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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Tantawy SI, Timofeeva N, Sarkar A, Gandhi V. Targeting MCL-1 protein to treat cancer: opportunities and challenges. Front Oncol 2023; 13:1226289. [PMID: 37601693 PMCID: PMC10436212 DOI: 10.3389/fonc.2023.1226289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 07/03/2023] [Indexed: 08/22/2023] Open
Abstract
Evading apoptosis has been linked to tumor development and chemoresistance. One mechanism for this evasion is the overexpression of prosurvival B-cell lymphoma-2 (BCL-2) family proteins, which gives cancer cells a survival advantage. Mcl-1, a member of the BCL-2 family, is among the most frequently amplified genes in cancer. Targeting myeloid cell leukemia-1 (MCL-1) protein is a successful strategy to induce apoptosis and overcome tumor resistance to chemotherapy and targeted therapy. Various strategies to inhibit the antiapoptotic activity of MCL-1 protein, including transcription, translation, and the degradation of MCL-1 protein, have been tested. Neutralizing MCL-1's function by targeting its interactions with other proteins via BCL-2 interacting mediator (BIM)S2A has been shown to be an equally effective approach. Encouraged by the design of venetoclax and its efficacy in chronic lymphocytic leukemia, scientists have developed other BCL-2 homology (BH3) mimetics-particularly MCL-1 inhibitors (MCL-1i)-that are currently in clinical trials for various cancers. While extensive reviews of MCL-1i are available, critical analyses focusing on the challenges of MCL-1i and their optimization are lacking. In this review, we discuss the current knowledge regarding clinically relevant MCL-1i and focus on predictive biomarkers of response, mechanisms of resistance, major issues associated with use of MCL-1i, and the future use of and maximization of the benefits from these agents.
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Affiliation(s)
- Shady I. Tantawy
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Natalia Timofeeva
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Aloke Sarkar
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Varsha Gandhi
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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Kari S, Murugesan A, Thiyagarajan R, Kidambi S, Razzokov J, Selvaraj C, Kandhavelu M, Marimuthu P. Bias-force guided simulations combined with experimental validations towards GPR17 modulators identification. Biomed Pharmacother 2023; 160:114320. [PMID: 36716660 DOI: 10.1016/j.biopha.2023.114320] [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: 12/10/2022] [Revised: 01/17/2023] [Accepted: 01/26/2023] [Indexed: 01/29/2023] Open
Abstract
Glioblastoma Multiforme (GBM) is known to be by far the most aggressive brain tumor to affect adults. The median survival rate of GBM patient's is < 15 months, while the GBM cells aggressively develop resistance to chemo- and radiotherapy with their self-renewal capacity which suggests the pressing need to develop novel preventative measures. We have recently proved that GPR17 -an orphan G protein-coupled receptor- is highly expressed on the GBM cell surface and it has a vital role to play in the disease progression. Despite the progress made on GBM downregulation, there still remain difficulties in developing a promising modulator for GPR17, till date. Here, we have performed robust virtual screening combined with biased-force pulling molecular dynamic (MD) simulations to predict high-affinity GPR17 modulators followed by experimental validation. Initially, the database containing 1379 FDA-approved drugs were screened against the orthosteric binding pocket of the GPR17. The external bias-potentials were then applied to the screened hits during the MD simulations which enabled to predict a spectrum of rupture peak force values that were used to select four approved drugs -ZINC000003792417 (Sacubitril), ZINC000014210457 (Victrelis), ZINC000001536109 (Pralatrexate) and ZINC000003925861 (Vorapaxar)- as top hits. The hits selected turns out to demonstrate unique dissociation pathways, interaction pattern, and change in polar network over time. Subsequently the selected hits with GPR17 were measured by inhibiting the forskolin-stimulated cAMP accumulation in GBM cell lines, LN229 and SNB19. The ex vivo validations shows that Sacubitril drug can act as a full agonist, while Vorapaxar functions as a partial agonist for GPR17. The pEC50 of Sacubitril was identified as 4.841 and 4.661 for LN229 and SNB19, respectively. Small interference of the RNA (siRNA)- silenced the GPR17 to further validate the targeted binding of Sacubitril with GPR17. In the current investigation, we have identified new repurposable GPR17 specific drugs which are likely to increase the opportunity to treat orphan deadly diseases.
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Affiliation(s)
- Sana Kari
- Molecular Signaling Group, Faculty of Medicine and Health Technology, Tampere University and BioMediTech, P.O.Box 553, 33101 Tampere, Finland
| | - Akshaya Murugesan
- Molecular Signaling Group, Faculty of Medicine and Health Technology, Tampere University and BioMediTech, P.O.Box 553, 33101 Tampere, Finland
| | - Ramesh Thiyagarajan
- Department of Basic Medical Sciences, College of Medicine, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Kingdom of Saudi Arabia
| | - Srivatsan Kidambi
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, 820 N 16th Street, 207 Othmer Hall, NE 68588, USA
| | - Jamoliddin Razzokov
- Institute of Fundamental and Applied Research, National Research University TIIAME, Kori Niyoziy 39, 100000 Tashkent, Uzbekistan; College of Engineering, Akfa University, Milliy Bog Street 264, 111221 Tashkent, Uzbekistan; Institute of Material Sciences, Academy of Sciences, Chingiz Aytmatov 2b, 100084 Tashkent, Uzbekistan; Department of Physics, National University of Uzbekistan, Universitet 4, 100174 Tashkent, Uzbekistan; Laboratory of Experimental Biophysics, Centre for Advanced Technologies, Universitet 7, 100174 Tashkent, Uzbekistan
| | - Chandrabose Selvaraj
- Department of Biotechnology, Division of Research and Innovation, Saveetha School of Engineering, SIMATS, Chennai 602105, Tamil Nadu, India
| | - Meenakshisundaram Kandhavelu
- Molecular Signaling Group, Faculty of Medicine and Health Technology, Tampere University and BioMediTech, P.O.Box 553, 33101 Tampere, Finland.
| | - Parthiban Marimuthu
- Pharmaceutical Science Laboratory (PSL - Pharmacy) and Structural Bioinformatics Laboratory (SBL - Biochemistry), Faculty of Science and Engineering, Åbo Akademi University, FI-20520 Turku, Finland.
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Mittal P, Singh S, Sinha R, Shrivastava A, Singh A, Singh IK. Myeloid cell leukemia 1 (MCL-1): Structural characteristics and application in cancer therapy. Int J Biol Macromol 2021; 187:999-1018. [PMID: 34339789 DOI: 10.1016/j.ijbiomac.2021.07.166] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/24/2021] [Accepted: 07/26/2021] [Indexed: 12/20/2022]
Abstract
Apoptosis, a major hallmark of cancer cells, regulates cellular fate and homeostasis. BCL-2 (B-cell CLL/Lymphoma 2) protein family is popularly known to mediate the intrinsic mode of apoptosis, of which MCL-1 is a crucial member. Myeloid cell leukemia 1 (MCL-1) is an anti-apoptotic oncoprotein and one of the most investigated members of the BCL-2 family. It is commonly known to be genetically altered, aberrantly overexpressed, and primarily associated with drug resistance in various human cancers. Recent advancements in the development of selective MCL-1 inhibitors and evaluating their effectiveness in cancer treatment establish its popularity as a molecular target. The overall aim is the selective induction of apoptosis in cancer cells by using a single or combination of BCL-2 family inhibitors. Delineating the precise molecular mechanisms associated with MCL-1-mediated cancer progression will certainly improve the efficacy of clinical interventions aimed at MCL-1 and hence patient survival. This review is structured to highlight the structural characteristics of MCL-1, its specific interactions with NOXA, MCL-1-regulatory microRNAs, and at the same time focus on the emerging therapeutic strategies targeting our protein of interest (MCL-1), alone or in combination with other treatments.
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Affiliation(s)
- Pooja Mittal
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi 110019, India
| | - Sujata Singh
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi 110019, India
| | - Rajesh Sinha
- Department of Dermatology, University of Alabama, Birmingham 35205, United States of America
| | - Anju Shrivastava
- Department of Zoology, University of Delhi, New Delhi, 110007, India
| | - Archana Singh
- Department of Botany, Hans Raj College, University of Delhi, New Delhi 110007, India.
| | - Indrakant Kumar Singh
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi 110019, India.
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Reddy CN, Manzar N, Ateeq B, Sankararamakrishnan R. Computational Design of BH3-Mimetic Peptide Inhibitors That Can Bind Specifically to Mcl-1 or Bcl-X L: Role of Non-Hot Spot Residues. Biochemistry 2020; 59:4379-4394. [PMID: 33146015 DOI: 10.1021/acs.biochem.0c00661] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Interactions between pro- and anti-apoptotic Bcl-2 proteins decide the fate of the cell. The BH3 domain of pro-apoptotic Bcl-2 proteins interacts with the exposed hydrophobic groove of their anti-apoptotic counterparts. Through their design and development, BH3 mimetics that target the hydrophobic groove of specific anti-apoptotic Bcl-2 proteins have the potential to become anticancer drugs. We have developed a novel computational method for designing sequences with BH3 domain features that can bind specifically to anti-apoptotic Mcl-1 or Bcl-XL. In this method, we retained the four highly conserved hydrophobic and aspartic residues of wild-type BH3 sequences and randomly substituted all other positions to generate a large number of BH3-like sequences. We modeled 20000 complex structures with Mcl-1 or Bcl-XL using the BH3-like sequences derived from five wild-type pro-apoptotic BH3 peptides. Peptide-protein interaction energies calculated from these models for each set of BH3-like sequences resulted in negatively skewed extreme value distributions. The selected BH3-like sequences from the extreme negative tail regions have highly favorable interaction energies with Mcl-1 or Bcl-XL. They are enriched in acidic and basic residues when they bind to Mcl-1 and Bcl-XL, respectively. With the charged residues often away from the binding interface, the overall electric field generated by the charged residues results in strong long-range electrostatic interaction energies between the peptide and the protein giving rise to high specificity. Cell viability studies of representative BH3-like peptides further validated the predicted specificity. This study has revealed the importance of non-hot spot residues in BH3-mimetic peptides in providing specificity to a particular anti-apoptotic protein.
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Predicted Hotspot Residues Involved in Allosteric Signal Transmission in Pro-Apoptotic Peptide-Mcl1 Complexes. Biomolecules 2020; 10:biom10081114. [PMID: 32731448 PMCID: PMC7463671 DOI: 10.3390/biom10081114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/16/2020] [Accepted: 07/24/2020] [Indexed: 11/30/2022] Open
Abstract
Mcl1 is a primary member of the Bcl–2 family—anti–apoptotic proteins (AAP)—that is overexpressed in several cancer pathologies. The apoptotic regulation is mediated through the binding of pro-apoptotic peptides (PAPs) (e.g., Bak and Bid) at the canonical hydrophobic binding groove (CBG) of Mcl1. Although all PAPs form amphipathic α-helices, their amino acid sequences vary to different degree. This sequence variation exhibits a central role in the binding partner selectivity towards different AAPs. Thus, constructing a novel peptide or small organic molecule with the ability to mimic the natural regulatory process of PAP is essential to inhibit various AAPs. Previously reported experimental binding free energies (BFEs) were utilized in the current investigation aimed to understand the mechanistic basis of different PAPs targeted to mMcl1. Molecular dynamics (MD) simulations used to estimate BFEs between mMcl1—PAP complexes using Molecular Mechanics-Generalized Born Solvent Accessible (MMGBSA) approach with multiple parameters. Predicted BFE values showed an excellent agreement with the experiment (R2 = 0.92). The van–der Waals (ΔGvdw) and electrostatic (ΔGele) energy terms found to be the main energy components that drive heterodimerization of mMcl1—PAP complexes. Finally, the dynamic network analysis predicted the allosteric signal transmission pathway involves more favorable energy contributing residues. In total, the results obtained from the current investigation may provide valuable insights for the synthesis of a novel peptide or small organic inhibitor targeting Mcl1.
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