1
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Baumann HM, Mobley DL. Impact of protein conformations on binding free energy calculations in the beta-secretase 1 system. J Comput Chem 2024; 45:2024-2033. [PMID: 38725239 PMCID: PMC11236511 DOI: 10.1002/jcc.27365] [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: 09/12/2023] [Revised: 01/13/2024] [Accepted: 03/24/2024] [Indexed: 07/11/2024]
Abstract
In binding free energy calculations, simulations must sample all relevant conformations of the system in order to obtain unbiased results. For instance, different ligands can bind to different metastable states of a protein, and if these protein conformational changes are not sampled in relative binding free energy calculations, the contribution of these states to binding is not accounted for and thus calculated binding free energies are inaccurate. In this work, we investigate the impact of different beta-sectretase 1 (BACE1) protein conformations obtained from x-ray crystallography on the binding of BACE1 inhibitors. We highlight how these conformational changes are not adequately sampled in typical molecular dynamics simulations. Furthermore, we show that insufficient sampling of relevant conformations induces substantial error in relative binding free energy calculations, as judged by a variation in calculated relative binding free energies up to 2 kcal/mol depending on the starting protein conformation. These results emphasize the importance of protein conformational sampling and pose this BACE1 system as a challenge case for further method development in the area of enhanced protein conformational sampling, either in combination with binding calculations or as an endpoint correction.
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Affiliation(s)
- Hannah M Baumann
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California, USA
| | - David L Mobley
- Department of Chemistry, University of California, Irvine, California, USA
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2
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Iqbal D, Alsaweed M, Jamal QMS, Asad MR, Rizvi SMD, Rizvi MR, Albadrani HM, Hamed M, Jahan S, Alyenbaawi H. Pharmacophore-Based Screening, Molecular Docking, and Dynamic Simulation of Fungal Metabolites as Inhibitors of Multi-Targets in Neurodegenerative Disorders. Biomolecules 2023; 13:1613. [PMID: 38002295 PMCID: PMC10669353 DOI: 10.3390/biom13111613] [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: 09/21/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
Neurodegenerative disorders, such as Alzheimer's disease (AD), negatively affect the economic and psychological system. For AD, there is still a lack of disease-altering treatments and promising cures due to its complex pathophysiology. In this study, we computationally screened the natural database of fungal metabolites against three known therapeutic target proteins of AD. Initially, a pharmacophore-based, drug-likeness category was employed for screening, and it filtered the 14 (A-N) best hits out of 17,544 fungal metabolites. The 14 best hits were docked individually against GSK-3β, the NMDA receptor, and BACE-1 to investigate the potential of finding a multitarget inhibitor. We found that compounds B, F, and L were immuno-toxic, whereas E, H, I, and J had a higher LD50 dose (5000 mg/kg). Among the examined metabolites, the Bisacremine-C (compound I) was found to be the most active molecule against GSK-3β (ΔG: -8.7 ± 0.2 Kcal/mol, Ki: 2.4 × 106 M-1), NMDA (ΔG: -9.5 ± 0.1 Kcal/mol, Ki: 9.2 × 106 M-1), and BACE-1 (ΔG: -9.1 ± 0.2 Kcal/mol, Ki: 4.7 × 106 M-1). It showed a 25-fold higher affinity with GSK-3β, 6.3-fold higher affinity with NMDA, and 9.04-fold higher affinity with BACE-1 than their native ligands, respectively. Molecular dynamic simulation parameters, such as RMSD, RMSF, Rg, and SASA, all confirmed that the overall structures of the targeted enzymes did not change significantly after binding with Bisacremine-C, and the ligand remained inside the binding cavity in a stable conformation for most of the simulation time. The most significant hydrophobic contacts for the GSK-3β-Bisacremine-C complex are with ILE62, VAL70, ALA83, and LEU188, whereas GLN185 is significant for H-bonds. In terms of hydrophobic contacts, TYR184 and PHE246 are the most important, while SER180 is vital for H-bonds in NMDA-Bisacremine-C. THR232 is the most crucial for H-bonds in BACE-1-Bisacremine-C and ILE110-produced hydrophobic contacts. This study laid a foundation for further experimental validation and clinical trials regarding the biopotency of Bisacremine-C.
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Affiliation(s)
- Danish Iqbal
- Department of Health Information Management, College of Applied Medical Sciences, Buraydah Private Colleges, Buraydah 51418, Saudi Arabia
| | - Mohammed Alsaweed
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah 11952, Saudi Arabia; (M.A.); (S.J.)
| | - Qazi Mohammad Sajid Jamal
- Department of Health Informatics, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia;
| | - Mohammad Rehan Asad
- Department of Basic Medical Science, College of Medicine, Majmaah University, Al Majmaah 11952, Saudi Arabia;
| | - Syed Mohd Danish Rizvi
- Department of Pharmaceutics, College of Pharmacy, University of Ha’il, Ha’il 81442, Saudi Arabia;
| | - Moattar Raza Rizvi
- School of Allied Health Sciences, Manav Rachna International Institute of Research & Studies (MRIIRS), Faridabad 121001, India;
| | - Hind Muteb Albadrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Imam Abdulrahman Bin Faisal University, Dammam 34212, Saudi Arabia;
| | - Munerah Hamed
- Department of Pathology, Faculty of Medicine, Umm Al-Qura University, Makkah 21955, Saudi Arabia;
| | - Sadaf Jahan
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah 11952, Saudi Arabia; (M.A.); (S.J.)
| | - Hadeel Alyenbaawi
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah 11952, Saudi Arabia; (M.A.); (S.J.)
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3
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Iqbal D, Rehman MT, Alajmi MF, Alsaweed M, Jamal QMS, Alasiry SM, Albaker AB, Hamed M, Kamal M, Albadrani HM. Multitargeted Virtual Screening and Molecular Simulation of Natural Product-like Compounds against GSK3β, NMDA-Receptor, and BACE-1 for the Management of Alzheimer's Disease. Pharmaceuticals (Basel) 2023; 16:ph16040622. [PMID: 37111379 PMCID: PMC10143309 DOI: 10.3390/ph16040622] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 04/18/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
The complexity of Alzheimer's disease (AD) and several side effects of currently available medication inclined us to search for a novel natural cure by targeting multiple key regulatory proteins. We initially virtually screened the natural product-like compounds against GSK3β, NMDA receptor, and BACE-1 and thereafter validated the best hit through molecular dynamics simulation (MDS). The results demonstrated that out of 2029 compounds, only 51 compounds exhibited better binding interactions than native ligands, with all three protein targets (NMDA, GSK3β, and BACE) considered multitarget inhibitors. Among them, F1094-0201 is the most potent inhibitor against multiple targets with binding energy -11.7, -10.6, and -12 kcal/mol, respectively. ADME-T analysis results showed that F1094-0201 was found to be suitable for CNS drug-likeness in addition to their other drug-likeness properties. The MDS results of RMSD, RMSF, Rg, SASA, SSE and residue interactions indicated the formation of a strong and stable association in the complex of ligands (F1094-0201) and proteins. These findings confirm the F1094-0201's ability to remain inside target proteins' binding pockets while forming a stable complex of protein-ligand. The free energies (MM/GBSA) of BACE-F1094-0201, GSK3β-F1094-0201, and NMDA-F1094-0201 complex formation were -73.78 ± 4.31 kcal mol-1, -72.77 ± 3.43 kcal mol-1, and -52.51 ± 2.85 kcal mol-1, respectively. Amongst the target proteins, F1094-0201 have a more stable association with BACE, followed by NMDA and GSK3β. These attributes of F1094-0201 indicate it as a possible option for the management of pathophysiological pathways associated with AD.
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Affiliation(s)
- Danish Iqbal
- Department of Health Information Management, College of Applied Medical Sciences, Buraydah Private Colleges, Buraydah 51418, Saudi Arabia
| | - Md Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mohamed F Alajmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mohammed Alsaweed
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah 11952, Saudi Arabia
| | - Qazi Mohammad Sajid Jamal
- Department of Health Informatics, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia
| | - Sharifa M Alasiry
- Critical Care Nursing, Department of Nursing, College of Applied Medical Sciences, Majmaah University, Al-Majmaah 15341, Saudi Arabia
| | - Awatif B Albaker
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Munerah Hamed
- Department of Pathology, Faculty of Medicine, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Mehnaz Kamal
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Hind Muteb Albadrani
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah 11952, Saudi Arabia
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4
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Sharma A, Bharate SB. Synthesis and Biological Evaluation of Coumarin Triazoles as Dual Inhibitors of Cholinesterases and β-Secretase. ACS OMEGA 2023; 8:11161-11176. [PMID: 37008108 PMCID: PMC10061512 DOI: 10.1021/acsomega.2c07993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/06/2023] [Indexed: 06/19/2023]
Abstract
Coumarin is a naturally occurring bioactive pharmacophore with wide occurrence among central nervous system (CNS)-active small molecules. 8-Acetylcoumarin, one of the natural coumarins, is a mild inhibitor of cholinesterases and β-secretase, which are vital targets of Alzheimer's disease. Herein, we synthesized a series of coumarin-triazole hybrids as potential multitargeted drug ligands (MTDLs) with better activity profiles. The coumarin-triazole hybrids occupy the cholinesterase active site gorge from the peripheral to the catalytic anionic site. The most active analogue, 10b, belonging to the 8-acetylcoumarin core, inhibits acetylcholinesterase (AChE), butyrylcholinesterase (BChE), and β-secretase-1 (BACE-1) with IC50 values of 2.57, 3.26, and 10.65 μM, respectively. The hybrid, 10b, crosses the blood-brain barrier via passive diffusion and inhibits the self-aggregation of amyloid-β monomers. The molecular dynamic simulation study reveals the strong interaction of 10b with three enzymes and forming stable complexes. Overall, the results warrant a detailed preclinical investigation of the coumarin-triazole hybrids.
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Affiliation(s)
- Ankita Sharma
- Natural
Products & Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
- Academy
of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sandip B. Bharate
- Natural
Products & Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
- Academy
of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
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5
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Nuthakki VK, Choudhary S, Reddy CN, Bhatt S, Jamwal A, Jotshi A, Raghuvanshi R, Sharma A, Thakur S, Jadhav HR, Bharate SS, Nandi U, Kumar A, Bharate SB. Design, Synthesis, and Pharmacological Evaluation of Embelin-Aryl/alkyl Amine Hybrids as Orally Bioavailable Blood-Brain Barrier Permeable Multitargeted Agents with Therapeutic Potential in Alzheimer's Disease: Discovery of SB-1448. ACS Chem Neurosci 2023; 14:1193-1219. [PMID: 36812360 DOI: 10.1021/acschemneuro.3c00030] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
The complex and multifaceted nature of Alzheimer's disease has brought about a pressing demand to develop ligands targeting multiple pathways to combat its outrageous prevalence. Embelin is a major secondary metabolite of Embelia ribes Burm f., one of the oldest herbs in Indian traditional medicine. It is a micromolar inhibitor of cholinesterases (ChEs) and β-site amyloid precursor protein cleaving enzyme 1 (BACE-1) with poor absorption, distribution, metabolism, and excretion (ADME) properties. Herein, we synthesize a series of embelin-aryl/alkyl amine hybrids to improve its physicochemical properties and therapeutic potency against targeted enzymes. The most active derivative, 9j (SB-1448), inhibits human acetylcholinesterase (hAChE), human butyrylcholinesterase (hBChE), and human BACE-1 (hBACE-1) with IC50 values of 0.15, 1.6, and 0.6 μM, respectively. It inhibits both ChEs noncompetitively with ki values of 0.21 and 1.3 μM, respectively. It is orally bioavailable, crosses blood-brain barrier (BBB), inhibits Aβ self-aggregation, possesses good ADME properties, and protects neuronal cells from scopolamine-induced cell death. The oral administration of 9j at 30 mg/kg attenuates the scopolamine-induced cognitive impairments in C57BL/6J mice.
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Affiliation(s)
- Vijay K Nuthakki
- Natural Products & Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sushil Choudhary
- Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Chilakala N Reddy
- Natural Products & Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Shipra Bhatt
- Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Ashiya Jamwal
- Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Anshika Jotshi
- Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India
| | - Rinky Raghuvanshi
- Natural Products & Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Ankita Sharma
- Natural Products & Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Shikha Thakur
- Department of Pharmacy, Birla Institute of Technology and Sciences Pilani, Pilani Campus, Vidya Vihar, Pilani 333031, Rajasthan, India
| | - Hemant R Jadhav
- Department of Pharmacy, Birla Institute of Technology and Sciences Pilani, Pilani Campus, Vidya Vihar, Pilani 333031, Rajasthan, India
| | - Sonali S Bharate
- Shobhaben Pratapbhai Patel School of Pharmacy & Technology Management, SVKM's NMIMS, V.L. Mehta Road, Vile Parle (W), Mumbai 400056, India
| | - Utpal Nandi
- Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Ajay Kumar
- Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sandip B Bharate
- Natural Products & Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
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6
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Raghuvanshi R, Jamwal A, Nandi U, Bharate SB. Multitargeted C9-substituted ester and ether derivatives of berberrubine for Alzheimer's disease: Design, synthesis, biological evaluation, metabolic stability, and pharmacokinetics. Drug Dev Res 2023; 84:121-140. [PMID: 36461610 DOI: 10.1002/ddr.22017] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/20/2022] [Accepted: 11/08/2022] [Indexed: 12/04/2022]
Abstract
Berberrubine is a naturally occurring isoquinoline alkaloid and a bioactive metabolite of berberine. Berberine exhibits a wide range of pharmacological activities, including cholinesterase inhibition. The cholinesterase inhibitors provide symptomatic treatment for Alzheimer's disease; however, multitarget-directed ligands have the potential as disease-modifying therapeutics. Herein, we prepared a series of C9-substituted berberrubine derivatives intending to discover dual cholinesterase and beta-site amyloid-precursor protein cleaving enzyme 1 (BACE-1) inhibitors. Most synthesized derivatives possessed balanced dual inhibition (AChE and BChE) activity in the submicromolar range and a moderate inhibition against BACE-1. Two most active ester derivatives, 12a and 11d, display inhibition of AChE, BChE, and BACE-1. The 3-methoxybenzoyl ester derivative, 12a, inhibits electric eel acetylcholinesterase (EeAChE), equine serum butyrylcholinesterase (eqBChE), and human hBACE-1 with IC50 values of 0.5, 4.3, and 11.9 μM, respectively and excellent BBB permeability (Pe = 8 × 10-6 cm/s). The ester derivative 12a is metabolically unstable; however, its ether analog 13 is stable in HLM and exhibits inhibition of AChE, BChE, and BACE-1 with IC50 values of 0.44, 3.8, and 17.9 μM, respectively. The ether analog also inhibits self-aggregation of Aβ and crosses BBB (Pe = 7.3 × 10-6 cm/s). Administration of 13 at 5 mg/kg (iv) in Wistar rats showed excellent plasma exposure with AUC0-∞ of 28,834 ng min/ml. In conclusion, the multitargeted berberrubine ether derivative 13 is CNS permeable and has good ADME properties.
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Affiliation(s)
- Rinky Raghuvanshi
- Natural Products & Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India.,Academy of Scientific & Innovative Research, Ghaziabad, India
| | - Ashiya Jamwal
- Academy of Scientific & Innovative Research, Ghaziabad, India.,Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India
| | - Utpal Nandi
- Academy of Scientific & Innovative Research, Ghaziabad, India.,Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India
| | - Sandip B Bharate
- Natural Products & Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India.,Academy of Scientific & Innovative Research, Ghaziabad, India
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7
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Guanidine-based β amyloid precursor protein cleavage enzyme 1 (BACE-1) inhibitors for the Alzheimer's disease (AD): A review. Bioorg Med Chem 2022; 74:117047. [DOI: 10.1016/j.bmc.2022.117047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/16/2022] [Accepted: 10/04/2022] [Indexed: 11/02/2022]
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8
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Kaur G, Goyal B. Deciphering the Molecular Mechanism of Inhibition of β‐Secretase (BACE1) Activity by a 2‐Amino‐imidazol‐4‐one Derivative. ChemistrySelect 2022. [DOI: 10.1002/slct.202202561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Gurmeet Kaur
- School of Chemistry & Biochemistry Thapar Institute of Engineering & Technology Patiala 147004 Punjab India
| | - Bhupesh Goyal
- School of Chemistry & Biochemistry Thapar Institute of Engineering & Technology Patiala 147004 Punjab India
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9
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Shrivastava SK, Nivrutti AA, Bhardwaj B, Waiker DK, Verma A, Tripathi PN, Tripathi M, Saraf P. Drug reposition-based design, synthesis, and biological evaluation of dual inhibitors of acetylcholinesterase and β-Secretase for treatment of Alzheimer's disease. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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10
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Patel S, Bansoad AV, Singh R, Khatik GL. BACE1: A Key Regulator in Alzheimer's Disease Progression and Current Development of its Inhibitors. Curr Neuropharmacol 2022; 20:1174-1193. [PMID: 34852746 PMCID: PMC9886827 DOI: 10.2174/1570159x19666211201094031] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/26/2021] [Accepted: 11/28/2021] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is a chronic neurodegenerative disease with no specific disease-modifying treatment. β-secretase (BACE1) is considered the potential and rationale target because it is involved in the rate-limiting step, which produces toxic Aβ42 peptides that leads to deposits in the form of amyloid plaques extracellularly, resulting in AD. OBJECTIVE This study aims to discuss the role and implications of BACE1 and its inhibitors in the management of AD. METHODS We have searched and collected the relevant quality work from PubMed using the following keywords "BACE1", BACE2", "inhibitors", and "Alzheimer's disease". In addition, we included the work which discusses the role of BACE1 in AD and the recent work on its inhibitors. RESULTS In this review, we have discussed the importance of BACE1 in regulating AD progression and the current development of BACE1 inhibitors. However, the development of a BACE1 inhibitor is very challenging due to the large active site of BACE1. Nevertheless, some of the BACE1 inhibitors have managed to enter advanced phases of clinical trials, such as MK-8931 (Verubecestat), E2609 (Elenbecestat), AZD3293 (Lanabecestat), and JNJ-54861911 (Atabecestat). This review also sheds light on the prospect of BACE1 inhibitors as the most effective therapeutic approach in delaying or preventing AD progression. CONCLUSION BACE1 is involved in the progression of AD. The current ongoing or failed clinical trials may help understand the role of BACE1 inhibition in regulating the Aβ load and cognitive status of AD patients.
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Affiliation(s)
| | - Ankush Vardhaman Bansoad
- Department of Pharmacology & Toxicology, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Bijnor-Sisendi Road, Sarojini Nagar, Near CRPF Base Camp, Lucknow (Uttar Pradesh), 226002, India
| | - Rakesh Singh
- Department of Pharmacology & Toxicology, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Bijnor-Sisendi Road, Sarojini Nagar, Near CRPF Base Camp, Lucknow (Uttar Pradesh), 226002, India
| | - Gopal L. Khatik
- Department of Medicinal Chemistry, ,Address correspondence to this author at the Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research- Raebareli, New Transit Campus, Bijnor-Sisendi Road, Sarojini Nagar, Near CRPF Base Camp, Lucknow, Uttar Pradesh, India, 226002; E-mail: ,
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11
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Taylor HA, Simmons KJ, Clavane EM, Trevelyan CJ, Brown JM, Przemyłska L, Watt NT, Matthews LC, Meakin PJ. PTPRD and DCC Are Novel BACE1 Substrates Differentially Expressed in Alzheimer's Disease: A Data Mining and Bioinformatics Study. Int J Mol Sci 2022; 23:ijms23094568. [PMID: 35562959 PMCID: PMC9103286 DOI: 10.3390/ijms23094568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/15/2022] [Accepted: 04/18/2022] [Indexed: 02/04/2023] Open
Abstract
The β-site Amyloid precursor protein Cleaving Enzyme 1 (BACE1) is an extensively studied therapeutic target for Alzheimer's disease (AD), owing to its role in the production of neurotoxic amyloid beta (Aβ) peptides. However, despite numerous BACE1 inhibitors entering clinical trials, none have successfully improved AD pathogenesis, despite effectively lowering Aβ concentrations. This can, in part, be attributed to an incomplete understanding of BACE1, including its physiological functions and substrate specificity. We propose that BACE1 has additional important physiological functions, mediated through substrates still to be identified. Thus, to address this, we computationally analysed a list of 533 BACE1 dependent proteins, identified from the literature, for potential BACE1 substrates, and compared them against proteins differentially expressed in AD. We identified 15 novel BACE1 substrates that were specifically altered in AD. To confirm our analysis, we validated Protein tyrosine phosphatase receptor type D (PTPRD) and Netrin receptor DCC (DCC) using Western blotting. These findings shed light on the BACE1 inhibitor failings and could enable the design of substrate-specific inhibitors to target alternative BACE1 substrates. Furthermore, it gives us a greater understanding of the roles of BACE1 and its dysfunction in AD.
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Affiliation(s)
- Hannah A. Taylor
- Leeds Institute of Cardiovascular and Metabolic Medicine, Faculty of Medicine and Health, University of Leeds, Leeds LS2 9JT, UK; (H.A.T.); (K.J.S.); (E.M.C.); (C.J.T.); (J.M.B.); (L.P.); (N.T.W.)
| | - Katie J. Simmons
- Leeds Institute of Cardiovascular and Metabolic Medicine, Faculty of Medicine and Health, University of Leeds, Leeds LS2 9JT, UK; (H.A.T.); (K.J.S.); (E.M.C.); (C.J.T.); (J.M.B.); (L.P.); (N.T.W.)
| | - Eva M. Clavane
- Leeds Institute of Cardiovascular and Metabolic Medicine, Faculty of Medicine and Health, University of Leeds, Leeds LS2 9JT, UK; (H.A.T.); (K.J.S.); (E.M.C.); (C.J.T.); (J.M.B.); (L.P.); (N.T.W.)
| | - Christopher J. Trevelyan
- Leeds Institute of Cardiovascular and Metabolic Medicine, Faculty of Medicine and Health, University of Leeds, Leeds LS2 9JT, UK; (H.A.T.); (K.J.S.); (E.M.C.); (C.J.T.); (J.M.B.); (L.P.); (N.T.W.)
| | - Jane M. Brown
- Leeds Institute of Cardiovascular and Metabolic Medicine, Faculty of Medicine and Health, University of Leeds, Leeds LS2 9JT, UK; (H.A.T.); (K.J.S.); (E.M.C.); (C.J.T.); (J.M.B.); (L.P.); (N.T.W.)
| | - Lena Przemyłska
- Leeds Institute of Cardiovascular and Metabolic Medicine, Faculty of Medicine and Health, University of Leeds, Leeds LS2 9JT, UK; (H.A.T.); (K.J.S.); (E.M.C.); (C.J.T.); (J.M.B.); (L.P.); (N.T.W.)
| | - Nicole T. Watt
- Leeds Institute of Cardiovascular and Metabolic Medicine, Faculty of Medicine and Health, University of Leeds, Leeds LS2 9JT, UK; (H.A.T.); (K.J.S.); (E.M.C.); (C.J.T.); (J.M.B.); (L.P.); (N.T.W.)
| | - Laura C. Matthews
- Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds LS2 9JT, UK;
| | - Paul J. Meakin
- Leeds Institute of Cardiovascular and Metabolic Medicine, Faculty of Medicine and Health, University of Leeds, Leeds LS2 9JT, UK; (H.A.T.); (K.J.S.); (E.M.C.); (C.J.T.); (J.M.B.); (L.P.); (N.T.W.)
- Correspondence:
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12
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Mishra P, Basak S, Mukherjee A, Basu A. Design and Study of In Silico Binding Dynamics of Certain Isoxazole Bearing Leads Against Aβ-42 and BACE-1 Loop in Protein Fibrillation. LETT DRUG DES DISCOV 2022. [DOI: 10.2174/1570180818666210813120444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Aims:
Design isoxazole bearing leads as dual inhibitors against Amyloid β and BACE-1 loop
in protein fibrillation.
Background:
Protein fibrillation is one of the key reasons for several diseases, namely Alzheimer’s, Parkinson’s,
and many others. One of the key strategies of preventing protein fibrillation is destabilizing the
protein fibrils themselves or inhibiting the amyloid fibril-forming pathway in the initial stage.
Introduction:
Attempts have been taken to design newer leads to inhibit protein fibrillation by targeting
the β-amyloidogenesis pathway in the brain. To exploit interfenestration between Amyloid β -42 protein
and BACE-1 (β-site amyloid precursor protein cleaving enzyme) for amyloidogenesis, studies are undertaken
to design dual inhibitors against the same.
Method:
In vitro binding interactions were found using docking, de novo ligand design, and MD simulation
study.
Results:
Three compounds bearing an isoxazole heterocyclic nucleus were designed which could successfully
bind to the hydrophobic raft and salt bridge residues Asp 23-Lys-26 of Amyloid β, destabilizing the
growing fibril. Additionally, one of our candidate compounds exhibited force of interaction with Thr232
at the S3 pocket of BACE-1, interacted with key residue Asp228, Tyr71, and Thr72 of the β-hairpin flap
and hydrogen bonding with Gly11 at loop 10s.
Conclusion:
Protein flexibility dynamics of the Aβ-42 protein revealed that there is a considerable conformational
change of the same with or without ligand binding. The lower RMSF of the bound region and
reprogramming residual contacts within the Aβ-42 protein suggested successful binding of the ligand with
the protein, lowering the access for further β-β dimerization.
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Affiliation(s)
- Puja Mishra
- Dr. B.C. Roy College of Pharmacy & Allied Health Sciences, Durgapur, WB, India
| | - Souvik Basak
- Dr. B.C. Roy College of Pharmacy & Allied Health Sciences, Durgapur, WB, India
| | - Arup Mukherjee
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, Kolkata, WB, India
| | - Anindya Basu
- School of Pharmaceutical Sciences, Rajiv
Gandhi Proudyogiki Vishwavidyalaya, Bhopal, India
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13
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Machauer R, Lueoend R, Hurth K, Veenstra SJ, Rueeger H, Voegtle M, Tintelnot-Blomley M, Rondeau JM, Jacobson LH, Laue G, Beltz K, Neumann U. Discovery of Umibecestat (CNP520): A Potent, Selective, and Efficacious β-Secretase (BACE1) Inhibitor for the Prevention of Alzheimer's Disease. J Med Chem 2021; 64:15262-15279. [PMID: 34648711 DOI: 10.1021/acs.jmedchem.1c01300] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
After identification of lead compound 6, 5-amino-1,4-oxazine BACE1 inhibitors were optimized in order to improve potency, brain penetration, and metabolic stability. Insertion of a methyl and a trifluoromethyl group at the 6-position of the 5-amino-1,4-oxazine led to 8 (NB-360), an inhibitor with a pKa of 7.1, a very low P-glycoprotein efflux ratio, and excellent pharmacological profile, enabling high central nervous system penetration and exposure. Fur color changes observed with NB-360 in efficacy studies in preclinical animal models triggered further optimization of the series. Herein, we describe the steps leading to the discovery of 3-chloro-5-trifluoromethyl-pyridine-2-carboxylic acid [6-((3R,6R)-5-amino-3,6-dimethyl-6-trifluoromethyl-3,6-dihydro-2H-[1,4]oxazin-3-yl)-5-fluoro-pyridin-2-yl]amide 15 (CNP520, umibecestat), an inhibitor with superior BACE1/BACE2 selectivity and pharmacokinetics. CNP520 reduced significantly Aβ levels in mice and rats in acute and chronic treatment regimens without any side effects and thus qualified for Alzheimer's disease prevention studies in the clinic.
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Affiliation(s)
- Rainer Machauer
- Global Discovery Chemistry, Novartis Pharma AG, CH-4056 Basel, Switzerland
| | - Rainer Lueoend
- Global Discovery Chemistry, Novartis Pharma AG, CH-4056 Basel, Switzerland
| | - Konstanze Hurth
- Global Discovery Chemistry, Novartis Pharma AG, CH-4056 Basel, Switzerland
| | - Siem J Veenstra
- Global Discovery Chemistry, Novartis Pharma AG, CH-4056 Basel, Switzerland
| | - Heinrich Rueeger
- Global Discovery Chemistry, Novartis Pharma AG, CH-4056 Basel, Switzerland
| | - Markus Voegtle
- Global Discovery Chemistry, Novartis Pharma AG, CH-4056 Basel, Switzerland
| | | | - Jean-Michel Rondeau
- Chemical Biology and Therapeutics, Structural Biology Platform, Novartis Pharma AG, CH-4056 Basel, Switzerland
| | - Laura H Jacobson
- Department of Neuroscience, Novartis Pharma AG, CH-4056 Basel, Switzerland
| | - Grit Laue
- Pharmacokinetic-Sciences, Novartis Institutes for BioMedical Research, Novartis Pharma AG, CH-4056 Basel, Switzerland
| | - Karen Beltz
- Pharmacokinetic-Sciences, Novartis Institutes for BioMedical Research, Novartis Pharma AG, CH-4056 Basel, Switzerland
| | - Ulf Neumann
- Department of Neuroscience, Novartis Pharma AG, CH-4056 Basel, Switzerland
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14
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Shah H, Patel A, Parikh V, Nagani A, Bhimani B, Shah U, Bambharoliya T. The β-Secretase Enzyme BACE1: A Biochemical Enigma for Alzheimer's Disease. CNS & NEUROLOGICAL DISORDERS DRUG TARGETS 2021; 19:184-194. [PMID: 32452328 DOI: 10.2174/1871527319666200526144141] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 04/18/2020] [Accepted: 04/29/2020] [Indexed: 01/08/2023]
Abstract
Beta site amyloid precursor protein cleaving enzyme 1 (BACE1) is a rational target in Alzheimer's Disease (AD) drug development due to its role in amyloidogenic cleavage of Amyloid Precursor Protein (APP) in generating Amyloid β (Aβ). This β-secretase cleaves not only Amyloid Precursor Protein (APP) and its homologues, but also small series of substrates including neuregulin and β subunit of voltage-gated sodium channel that play a very important role in the development and normal function of the brain. Moreover, BACE1 is modulated at the post-translational level by several factors that are associated with both physiological and pathological functions. Since the discovery of BACE1 over a decade ago, medicinal chemistry and pharmacokinetics of BACE1 small molecule inhibitors have proven challenging for the treatment of Alzheimer's disease.
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Affiliation(s)
- Hirak Shah
- Department of Pharmaceutical Chemistry, Parul Institute of Pharmacy, Parul University, Vadodara, Gujarat 391760, India
| | - Ashish Patel
- Ramanbhai Patel College of Pharmacy, Charotar University of Science and Technology, Changa, Gujarat 388421, India
| | - Vruti Parikh
- Department of Pharmaceutical Chemistry, Parul Institute of Pharmacy, Parul University, Vadodara, Gujarat 391760, India
| | - Afzal Nagani
- Department of Pharmaceutical Chemistry, Parul Institute of Pharmacy, Parul University, Vadodara, Gujarat 391760, India
| | - Bhargav Bhimani
- Piramal Discovery Solution, Pharmaceutical Special Economic Zone, Ahmedabad 382213, India
| | - Umang Shah
- Ramanbhai Patel College of Pharmacy, Charotar University of Science and Technology, Changa, Gujarat 388421, India
| | - Tushar Bambharoliya
- Pharmaceutical Polymer Technology, North Carolina State University, North Carolina, NC, United States
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15
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Bhakat S. Pepsin-like aspartic proteases (PAPs) as model systems for combining biomolecular simulation with biophysical experiments. RSC Adv 2021; 11:11026-11047. [PMID: 35423571 PMCID: PMC8695779 DOI: 10.1039/d0ra10359d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/21/2021] [Indexed: 01/26/2023] Open
Abstract
Pepsin-like aspartic proteases (PAPs) are a class of aspartic proteases which shares tremendous structural similarity with human pepsin. One of the key structural features of PAPs is the presence of a β-hairpin motif otherwise known as flap. The biological function of the PAPs is highly dependent on the conformational dynamics of the flap region. In apo PAPs, the conformational dynamics of the flap is dominated by the rotational degrees of freedom associated with χ1 and χ2 angles of conserved Tyr (or Phe in some cases). However it is plausible that dihedral order parameters associated with several other residues might play crucial roles in the conformational dynamics of apo PAPs. Due to their size, complexities associated with conformational dynamics and clinical significance (drug targets for malaria, Alzheimer's disease etc.), PAPs provide a challenging testing ground for computational and experimental methods focusing on understanding conformational dynamics and molecular recognition in biomolecules. The opening of the flap region is necessary to accommodate substrate/ligand in the active site of the PAPs. The BIG challenge is to gain atomistic details into how reversible ligand binding/unbinding (molecular recognition) affects the conformational dynamics. Recent reports of kinetics (K i, K d) and thermodynamic parameters (ΔH, TΔS, and ΔG) associated with macro-cyclic ligands bound to BACE1 (belongs to PAP family) provide a perfect challenge (how to deal with big ligands with multiple torsional angles and select optimum order parameters to study reversible ligand binding/unbinding) for computational methods to predict binding free energies and kinetics beyond typical test systems e.g. benzamide-trypsin. In this work, i reviewed several order parameters which were proposed to capture the conformational dynamics and molecular recognition in PAPs. I further highlighted how machine learning methods can be used as order parameters in the context of PAPs. I then proposed some open ideas and challenges in the context of molecular simulation and put forward my case on how biophysical experiments e.g. NMR, time-resolved FRET etc. can be used in conjunction with biomolecular simulation to gain complete atomistic insights into the conformational dynamics of PAPs.
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Affiliation(s)
- Soumendranath Bhakat
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University P. O. Box 124 SE-22100 Lund Sweden +46-769608418
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16
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Smith RD, Carlson HA. Identification of Cryptic Binding Sites Using MixMD with Standard and Accelerated Molecular Dynamics. J Chem Inf Model 2021; 61:1287-1299. [PMID: 33599485 DOI: 10.1021/acs.jcim.0c01002] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Protein dynamics play an important role in small molecule binding and can pose a significant challenge in the identification of potential binding sites. Cryptic binding sites have been defined as sites which require significant rearrangement of the protein structure to become physically accessible to a ligand. Mixed-solvent MD (MixMD) is a computational protocol which maps the surface of the protein using molecular dynamics (MD) of the unbound protein solvated in a 5% box of probe molecules with explicit water. This method has successfully identified known active and allosteric sites which did not require reorganization. In this study, we apply the MixMD protocol to identify known cryptic sites of 12 proteins characterized by a wide range of conformational changes. Of these 12 proteins, three require reorganization of side chains, five require loop movements, and four require movement of more significant structures such as whole helices. In five cases, we find that standard MixMD simulations are able to map the cryptic binding sites with at least one probe type. In two cases (guanylate kinase and TIE-2), accelerated MD, which increases sampling of torsional angles, was necessary to achieve mapping of portions of the cryptic binding site missed by standard MixMD. For more complex systems where movement of a helix or domain is necessary, MixMD was unable to map the binding site even with accelerated dynamics, possibly due to the limited timescale (100 ns for individual simulations). In general, similar conformational dynamics are observed in water-only simulations and those with probe molecules. This could imply that the probes are not driving opening events but rather take advantage of mapping sites that spontaneously open as part of their inherent conformational behavior. Finally, we show that docking to an ensemble of conformations from the standard MixMD simulations performs better than docking the apo crystal structure in nine cases and even better than half of the bound crystal structures. Poorer performance was seen in docking to ensembles of conformations from the accelerated MixMD simulations.
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Affiliation(s)
- Richard D Smith
- Department of Medicinal Chemistry, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109-1056, United States
| | - Heather A Carlson
- Department of Medicinal Chemistry, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109-1056, United States
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17
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Ugbaja SC, Appiah-Kubi P, Lawal MM, Gumede NS, Kumalo HM. Unravelling the molecular basis of AM-6494 high potency at BACE1 in Alzheimer's disease: an integrated dynamic interaction investigation. J Biomol Struct Dyn 2021; 40:5253-5265. [PMID: 33410374 DOI: 10.1080/07391102.2020.1869099] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
β-amyloid precursor protein cleaving enzyme1 (BACE1) has prominently been an important drug design target implicated in Alzheimer's disease pathway. The failure rate of most of the already tested drugs at different clinical phases remains a major concern. Recently, AM-6494 was reported as a novel potent, highly selective, and orally effective inhibitor against BACE1. AM-6494 displayed no alteration of skin/fur colour in animal studies, an adverse effect common to previous BACE1 inhibitors. However, the atomistic molecular mechanism of BACE1 inhibition by AM-6494 remains unclear. To elucidate the binding mechanism of AM-6494 relative to umibecestat (CNP-520) as well as the structural changes when bound to BACE1, advanced computational techniques such as accelerated MD simulation and principal component analysis have been utilised. The results demonstrated higher binding affinity of AM-6494 at BACE1 with van der Waals as dominant energy contributor compared to umibecestat. Conformational monitoring of the β-hairpin flap covering the active site revealed an effective flap closure when bound with AM-6494 compared to CNP-520, which predominantly alternates between semi-open and closed conformations. The observed effective flap closure of AM-6494 explains its higher inhibitory power towards BACE1. Besides the catalytic Asp32/228 dyad, Tyr14, Leu30, Tyr71 and Gly230 represent critical residues in the potency of these inhibitors at BACE1 binding interface. The findings highlighted in this research provide a basis to explain AM-6494 high inhibitory potency and might assist in the design of new inhibitors with improved selectivity and potency for BACE1.
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Affiliation(s)
- Samuel C Ugbaja
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
| | - Patrick Appiah-Kubi
- Discipline of Pharmaceutical Sciences, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Monsurat M Lawal
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
| | - Nelisiwe S Gumede
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
| | - Hezekiel M Kumalo
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
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18
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Dheer D, Behera C, Singh D, Abdullaha M, Chashoo G, Bharate SB, Gupta PN, Shankar R. Design, synthesis and comparative analysis of triphenyl-1,2,3-triazoles as anti-proliferative agents. Eur J Med Chem 2020; 207:112813. [DOI: 10.1016/j.ejmech.2020.112813] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/18/2020] [Accepted: 09/02/2020] [Indexed: 12/12/2022]
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19
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Iida S, Nakamura HK, Mashimo T, Fukunishi Y. Structural Fluctuations of Aromatic Residues in an Apo-Form Reveal Cryptic Binding Sites: Implications for Fragment-Based Drug Design. J Phys Chem B 2020; 124:9977-9986. [PMID: 33140952 DOI: 10.1021/acs.jpcb.0c04963] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cryptic sites are binding pockets that are transiently formed in an apo form or that are induced by ligand binding. The investigation of cryptic sites is crucial for drug discovery, since these sites are ubiquitous in disease-related human proteins, and targeting them expands the number of drug targets greatly. However, although many computational studies have attempted to identify cryptic sites, the detection remains challenging. Here, we aimed to characterize and detect cryptic sites in terms of structural fluctuations in an apo form, investigating proteins each of which possesses a cryptic site. From their X-ray structures, we saw that aromatic residues tended to be found in cryptic sites. To examine structural fluctuations of the apo forms, we performed molecular dynamics (MD) simulations, producing probability distributions of the solvent-accessible surface area per aromatic residue. To detect aromatic residues in cryptic sites, we have proposed a "cryptic-site index" based on the distribution, demonstrating the performance via several measures, such as recall and specificity. Besides, we found that high-ranking aromatic residues were likely to probe concaves in a cryptic site. This implies that such fluctuations provide a profile of scaffolds of compounds with the potential to bind to a particular cryptic site.
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Affiliation(s)
- Shinji Iida
- Technology Research Association for Next-Generation Natural Products Chemistry, 2-3-26, Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Hironori K Nakamura
- Biomodeling Research Co., Ltd., 1-704-2, Uedanishi, Tenpaku-ku, Nagoya, Aichi 468-0058, Japan
| | - Tadaaki Mashimo
- Technology Research Association for Next-Generation Natural Products Chemistry, 2-3-26, Aomi, Koto-ku, Tokyo 135-0064, Japan.,IMSBIO Co., Ltd., 4-21-1, Higashiikebukuro, Toshima-ku, Tokyo 170-0013, Japan
| | - Yoshifumi Fukunishi
- Cellular and Molecular Biotechnology Research Institute, AIST Tokyo Waterfront, 2-3-26 Aomi, Koto-ku, Tokyo 135-0064, Japan
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20
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Zhao J, Liu X, Xia W, Zhang Y, Wang C. Targeting Amyloidogenic Processing of APP in Alzheimer's Disease. Front Mol Neurosci 2020; 13:137. [PMID: 32848600 PMCID: PMC7418514 DOI: 10.3389/fnmol.2020.00137] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 07/08/2020] [Indexed: 12/11/2022] Open
Abstract
Alzheimer's disease (AD) is the most common type of senile dementia, characterized by neurofibrillary tangle and amyloid plaque in brain pathology. Major efforts in AD drug were devoted to the interference with the production and accumulation of amyloid-β peptide (Aβ), which plays a causal role in the pathogenesis of AD. Aβ is generated from amyloid precursor protein (APP), by consecutive cleavage by β-secretase and γ-secretase. Therefore, β-secretase and γ-secretase inhibition have been the focus for AD drug discovery efforts for amyloid reduction. Here, we review β-secretase inhibitors and γ-secretase inhibitors/modulators, and their efficacies in clinical trials. In addition, we discussed the novel concept of specifically targeting the γ-secretase substrate APP. Targeting amyloidogenic processing of APP is still a fundamentally sound strategy to develop disease-modifying AD therapies and recent advance in γ-secretase/APP complex structure provides new opportunities in designing selective inhibitors/modulators for AD.
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Affiliation(s)
- Jing Zhao
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Xinyue Liu
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Weiming Xia
- Geriatric Research Education Clinical Center, Edith Nourse Rogers Memorial Veterans Hospital, Bedford, MA, United States
- Department of Pharmacology and Experimental Therapeutics, School of Medicine, Boston University, Boston, MA, United States
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, NY, United States
| | - Chunyu Wang
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, United States
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, United States
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21
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Sosibo S, Amoako DG, Somboro AM, Sun DD, Ngila JC, Kumalo H. Understanding the Binding Mechanism of Antagonist (AZD3293) Against BACE-1: Molecular Insights into Alzheimer’s Drug Discovery. LETT DRUG DES DISCOV 2020. [DOI: 10.2174/1570180816666191029142640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
β-site amyloid precursor protein cleaving enzyme (BACE 1) is the ratelimiting
enzyme in the formation of neurotoxic β-amyloid (Aβ) residues (Aβ1-40 or Aβ1-42)
considered as key players in the onset of Alzheimer’s Disease (AD). Consequently, BACE 1 is one
of the principal targets of anti-AD therapy with many small molecule BACE 1 inhibitors (BACE
1Is) in clinical trials. AZD3293 (Lanabecestat) is a BACE 1I that concluded in phase 2/3 clinical
trials. Due to the limited knowledge about the interaction of this drug with the BACE 1 enzyme, in
the present study, we performed comprehensive Molecular Dynamics (MD) analysis to understand
the binding mechanism of AZD3293 to BACE 1.
Methods:
A production run of 120 ns is carried out and results are analysed using Root Mean
Square Deviation (RMSD), root mean square fluctuation (RMSF), and radius of gyration (Rg) to
explain the stability of enzyme ligand complex. Further, the distance (d1) between the flap tip
(Thr72) and the hinge residue of the flexible loop (Thr328), in relation to θ1 (Thr72–Asp228-
Thr328), and to the dihedral angle δ (Thr72-Asp35-Asp228-Thr328) were measured.
Results:
The presence of the ligand within the active site restricted conformational changes as
shown by decreased values of RMSF and average RMSD of atomic positions when compared to the
values of the apoenzyme. Further analysis via the flap dynamics approach revealed that the
AZD3293 decreases the flexibility of binding residues and made them rigid by altering the
conformational changes.
Conclusion:
The prospective binding modes of AZD3293 from this study may extend the
knowledge of the BACE 1-drug interaction and pave the way to design analogues with similar
inhibitory properties needed to slow the progression of Alzheimer’s disease.
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Affiliation(s)
- Sphelele Sosibo
- School of Applied Chemistry, University of Johannesburg, Doornfontein, Johannesburg 2001, South Africa
| | - Daniel Gyamfi Amoako
- Drug Research and Innovation Research Unit, School of Medical Biochemistry, University of KwaZulu-Natal, Westville, Durban 4001, South Africa
| | - Anou Moise Somboro
- Drug Research and Innovation Research Unit, School of Medical Biochemistry, University of KwaZulu-Natal, Westville, Durban 4001, South Africa
| | - Darren Delai Sun
- School of Applied Chemistry, University of Johannesburg, Doornfontein, Johannesburg 2001, South Africa
| | - Jane Catherine Ngila
- School of Applied Chemistry, University of Johannesburg, Doornfontein, Johannesburg 2001, South Africa
| | - Hezekiel Kumalo
- Drug Research and Innovation Research Unit, School of Medical Biochemistry, University of KwaZulu-Natal, Westville, Durban 4001, South Africa
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22
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Frohn M, Liu L, Siegmund AC, Qian W, Amegadzie A, Chen N, Tan H, Hickman D, Wood S, Wen PH, Bartberger MD, Whittington DA, Allen JR, Bourbeau MP. The development of a structurally distinct series of BACE1 inhibitors via the (Z)-fluoro-olefin amide bioisosteric replacement. Bioorg Med Chem Lett 2020; 30:127240. [DOI: 10.1016/j.bmcl.2020.127240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/24/2020] [Accepted: 05/01/2020] [Indexed: 01/02/2023]
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23
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Mouchlis VD, Melagraki G, Zacharia LC, Afantitis A. Computer-Aided Drug Design of β-Secretase, γ-Secretase and Anti-Tau Inhibitors for the Discovery of Novel Alzheimer's Therapeutics. Int J Mol Sci 2020; 21:E703. [PMID: 31973122 PMCID: PMC7038192 DOI: 10.3390/ijms21030703] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/15/2020] [Accepted: 01/17/2020] [Indexed: 12/14/2022] Open
Abstract
Aging-associated neurodegenerative diseases, which are characterized by progressive neuronal death and synapses loss in human brain, are rapidly growing affecting millions of people globally. Alzheimer's is the most common neurodegenerative disease and it can be caused by genetic and environmental risk factors. This review describes the amyloid-β and Tau hypotheses leading to amyloid plaques and neurofibrillary tangles, respectively which are the predominant pathways for the development of anti-Alzheimer's small molecule inhibitors. The function and structure of the druggable targets of these two pathways including β-secretase, γ-secretase, and Tau are discussed in this review article. Computer-Aided Drug Design including computational structure-based design and ligand-based design have been employed successfully to develop inhibitors for biomolecular targets involved in Alzheimer's. The application of computational molecular modeling for the discovery of small molecule inhibitors and modulators for β-secretase and γ-secretase is summarized. Examples of computational approaches employed for the development of anti-amyloid aggregation and anti-Tau phosphorylation, proteolysis and aggregation inhibitors are also reported.
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Affiliation(s)
| | - Georgia Melagraki
- Division of Physical Sciences & Applications, Hellenic Military Academy, Vari 16672, Greece;
| | - Lefteris C. Zacharia
- Department of Life and Health Sciences, University of Nicosia, Nicosia 1700, Cyprus;
| | - Antreas Afantitis
- Department of ChemoInformatics, NovaMechanics Ltd., Nicosia 1046, Cyprus
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24
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Maesako M, Zoltowska KM, Berezovska O. Synapsin 1 promotes Aβ generation via BACE1 modulation. PLoS One 2019; 14:e0226368. [PMID: 31830091 PMCID: PMC6907790 DOI: 10.1371/journal.pone.0226368] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 11/25/2019] [Indexed: 12/26/2022] Open
Abstract
It has been revealed that β-amyloid (Aβ) is generated and released from the presynaptic terminals in activity-dependent manner. However, molecules modulating the presynaptic Aβ generation remain elusive. Here we test the hypothesis that Synapsin 1 (Syn1) may acts as a modulator of the Aβ production. Using biochemical and Förster resonance energy transfer (FRET)-based imaging approaches we have found that Syn1 knock down decreases, whereas (over)expression of Syn1 in cells increases the Aβ levels. Mechanistically, Syn1 does not seem to affect the activity of Presenilin 1 (PS1)/γ-secretase, PS1 conformation, or the proximity between PS1 and amyloid precursor protein (APP). However, we found that Syn1 is involved in up-regulation of the β-site APP cleaving enzyme 1 (BACE1)/β-secretase activity and increases the APP/BACE1 interaction. Therefore, we conclude that Syn1 may promote Aβ production via the modulation of BACE1.
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Affiliation(s)
- Masato Maesako
- MassGeneral Institute for Neurodegenerative Disease, Alzheimer’s Disease Research Unit, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, United States of America
| | - Katarzyna M. Zoltowska
- MassGeneral Institute for Neurodegenerative Disease, Alzheimer’s Disease Research Unit, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, United States of America
| | - Oksana Berezovska
- MassGeneral Institute for Neurodegenerative Disease, Alzheimer’s Disease Research Unit, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, United States of America
- * E-mail:
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Molecular insights into the inhibitory mechanism of bi-functional bis-tryptoline triazole against β-secretase (BACE1) enzyme. Amino Acids 2019; 51:1593-1607. [PMID: 31654211 DOI: 10.1007/s00726-019-02797-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 10/04/2019] [Indexed: 02/07/2023]
Abstract
The β-site amyloid precursor protein-cleaving enzyme 1 (β-secretase, BACE1) is involved in the formation of amyloid-β (Aβ) peptide that aggregates into soluble oligomers, amyloid fibrils, and plaques responsible for the neurodegeneration in Alzheimer disease (AD). BACE1 is one of the prime therapeutic targets for the design of inhibitors against AD as BACE1 participate in the rate-limiting step in Aβ production. Jiaranaikulwanitch et al. reported bis-tryptoline triazole (BTT) compound as a potent inhibitor against BACE1, Aβ aggregation as well as possessing metal chelation and antioxidant activity. However, the molecular mechanism of BACE1 inhibition by BTT remains unclear. Thus, molecular docking and molecular dynamics (MD) simulations were performed to elucidate the inhibitory mechanism of BTT against BACE1. MD simulations highlight that BTT interact with catalytic aspartic dyad residues (Asp32 and Asp228) and active pocket residues of BACE1. The hydrogen-bond interactions, hydrophobic contacts, and π-π stacking interactions of BTT with flap residues (Val67-Asp77) of BACE1 confine the movement of the flap and help to achieve closed (non-active) conformation. The PCA analysis highlights lower conformational fluctuations for BACE1-BTT complex, which suggests enhanced conformational stability in comparison to apo-BACE1. The results of the present study provide key insights into the underlying inhibitory mechanism of BTT against BACE1 and will be helpful for the rational design of novel inhibitors with enhanced potency against BACE1.
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26
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Pettus LH, Bourbeau MP, Bradley J, Bartberger MD, Chen K, Hickman D, Johnson M, Liu Q, Manning JR, Nanez A, Siegmund AC, Wen PH, Whittington DA, Allen JR, Wood S. Discovery of AM-6494: A Potent and Orally Efficacious β-Site Amyloid Precursor Protein Cleaving Enzyme 1 (BACE1) Inhibitor with in Vivo Selectivity over BACE2. J Med Chem 2019; 63:2263-2281. [DOI: 10.1021/acs.jmedchem.9b01034] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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27
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Influence of functional moiety in lupane-type triterpenoids in BACE1 inhibition. Comput Biol Chem 2019; 83:107101. [PMID: 31442708 DOI: 10.1016/j.compbiolchem.2019.107101] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/05/2019] [Accepted: 08/08/2019] [Indexed: 11/21/2022]
Abstract
Lupane-type triterpenoids have shown a potential effect against neurodegenerative disorders. Alzheimer's disease, one of the common neurodegenerative disease, is evident by the accumulation of amyloid-beta (Aβ) plaque in the extracellular regions of the brain. β-site amyloid precursor protein cleaving enzyme 1 (BACE1) is a key enzyme for the Aβ formation viathe cleavage of amyloid precursor protein (APP). Therefore, to find the potent BACE1 inhibitors and furthermore to explore the role of the functional group responsible for the strong BACE1 inhibitory activity, we synthesized a series of triterpenoids with lupane skeleton starting from the natural compounds calenduladiol and lupeol. Compound 1 revealed a potent competitive BACE1 inhibitory activity (IC50 = 16.77 ± 1.16 μM; Ki = 19.38). Furthermore, the molecular docking simulation revealed the importance of Tyr198 residue along with the other hydrophobic interactions for the strong affinity of 1‒BACE1 complex. To sum up, our results demonstrated the importance of carbonyl moiety at 3 and 16 position of lupane-type triterpenoid over the hydroxyl group at the same position.
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28
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Moussa-Pacha NM, Abdin SM, Omar HA, Alniss H, Al-Tel TH. BACE1 inhibitors: Current status and future directions in treating Alzheimer's disease. Med Res Rev 2019; 40:339-384. [PMID: 31347728 DOI: 10.1002/med.21622] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 05/22/2019] [Accepted: 06/13/2019] [Indexed: 12/28/2022]
Abstract
Alzheimer's disease (AD) is an irreversible, progressive neurodegenerative brain disorder with no current cure. One of the important therapeutic approaches of AD is the inhibition of β-site APP cleaving enzyme-1 (BACE1), which is involved in the rate-limiting step of the cleavage process of the amyloid precursor protein (APP) leading to the generation of the neurotoxic amyloid β (Aβ) protein after the γ-secretase completes its function. The produced insoluble Aβ aggregates lead to plaques deposition and neurodegeneration. BACE1 is, therefore, one of the attractive targets for the treatment of AD. This approach led to the development of potent BACE1 inhibitors, many of which were advanced to late stages in clinical trials. Nonetheless, the high failure rate of lead drug candidates targeting BACE1 brought to the forefront the need for finding new targets to uncover the mystery behind AD. In this review, we aim to discuss the most promising classes of BACE1 inhibitors with a description and analysis of their pharmacodynamic and pharmacokinetic parameters, with more focus on the lead drug candidates that reached late stages of clinical trials, such as MK8931, AZD-3293, JNJ-54861911, E2609, and CNP520. In addition, the manuscript discusses the safety concerns and insignificant physiological effects, which were highlighted for the most successful BACE1 inhibitors. Furthermore, the review demonstrates with increasing evidence that despite tremendous efforts and promising results conceived with BACE1 inhibitors, the latest studies suggest that their clinical use for treating Alzheimer's disease should be reconsidered. Finally, the review sheds light on alternative therapeutic options for targeting AD.
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Affiliation(s)
- Nour M Moussa-Pacha
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Shifaa M Abdin
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Hany A Omar
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates.,College of Pharmacy and College of Medicine, University of Sharjah, Sharjah, United Arab Emirates.,Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - Hasan Alniss
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates.,College of Pharmacy and College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Taleb H Al-Tel
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates.,College of Pharmacy and College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
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29
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Paudel P, Seong SH, Zhou Y, Ha MT, Min BS, Jung HA, Choi JS. Arylbenzofurans from the Root Bark of Morus alba as Triple Inhibitors of Cholinesterase, β-Site Amyloid Precursor Protein Cleaving Enzyme 1, and Glycogen Synthase Kinase-3β: Relevance to Alzheimer's Disease. ACS OMEGA 2019; 4:6283-6294. [PMID: 31459768 PMCID: PMC6649263 DOI: 10.1021/acsomega.9b00198] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 03/25/2019] [Indexed: 05/07/2023]
Abstract
Cholinesterase, β-site amyloid precursor protein cleaving enzyme 1 (BACE1), and glycogen synthase kinase-3β (GSK-3β) are the three main enzymes responsible for the early onset of Alzheimer's disease (AD). The main aim of the present study was to delineate and accentuate the triple-inhibitory potential of arylbenzofurans from Morus alba against these enzymes. Overall, the enzyme inhibition assays demonstrated the prominence of mulberrofuran D2 as an inhibitor of AChE, BChE, BACE1, and GSK-3β enzymes with IC50 values of 4.61, 1.51, 0.73, and 6.36 μM, respectively. Enzyme kinetics revealed different modes of inhibition, and in silico modeling suggested that mulberrofuran D2 inhibited these enzymes with low binding energy through hydrophilic, hydrophobic, and π-cation interactions in the active site cavities. Similarly, in Aβ-aggregation assays, mulberrofuran D2 inhibited self-induced and AChE-induced Aβ aggregation in a concentration-dependent manner that was superior to reference drugs. These results suggest that arylbenzofurans from M. alba, especially mulberrofuran D2, are triple inhibitors of cholinesterase, BACE1, and GSK-3β and may represent a novel class of anti-AD drugs.
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Affiliation(s)
- Pradeep Paudel
- Department
of Food and Life Science, Pukyong National
University, Busan 48513, Republic of Korea
| | - Su Hui Seong
- Department
of Food and Life Science, Pukyong National
University, Busan 48513, Republic of Korea
| | - Yajuan Zhou
- Department
of Food and Life Science, Pukyong National
University, Busan 48513, Republic of Korea
| | - Manh Tuan Ha
- College
of Pharmacy, Drug Research and Development Center, Catholic University of Daegu, Gyeongbuk 38430, Republic of Korea
| | - Byung Sun Min
- College
of Pharmacy, Drug Research and Development Center, Catholic University of Daegu, Gyeongbuk 38430, Republic of Korea
| | - Hyun Ah Jung
- Department
of Food Science and Human Nutrition, Chonbuk
National University, Jeonju 54896, Republic of Korea
- E-mail: . Tel: +82-63-270-4882 (H.A.J.)
| | - Jae Sue Choi
- Department
of Food and Life Science, Pukyong National
University, Busan 48513, Republic of Korea
- E-mail: . Tel: +82-51-629-5845 (J.S.C.)
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30
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Fujimoto K, Matsuoka E, Asada N, Tadano G, Yamamoto T, Nakahara K, Fuchino K, Ito H, Kanegawa N, Moechars D, Gijsen HJM, Kusakabe KI. Structure-Based Design of Selective β-Site Amyloid Precursor Protein Cleaving Enzyme 1 (BACE1) Inhibitors: Targeting the Flap to Gain Selectivity over BACE2. J Med Chem 2019; 62:5080-5095. [DOI: 10.1021/acs.jmedchem.9b00309] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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31
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Design and development of multitarget-directed N-Benzylpiperidine analogs as potential candidates for the treatment of Alzheimer's disease. Eur J Med Chem 2019; 167:510-524. [DOI: 10.1016/j.ejmech.2019.02.030] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/08/2019] [Accepted: 02/09/2019] [Indexed: 11/20/2022]
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32
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Hu H, Chen Z, Xu X, Xu Y. Structure-Based Survey of the Binding Modes of BACE1 Inhibitors. ACS Chem Neurosci 2019; 10:880-889. [PMID: 30540177 DOI: 10.1021/acschemneuro.8b00420] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
BACE1 is a key aspartic protease that cleaves the amyloid precursor protein to generate of the amyloid peptide that is believed to be responsible for the Alzheimer's disease amyloid cascade. It is thus recognized as a promising therapeutic target for Alzheimer's disease treatment, and large efforts have been made in the discovery of novel BACE1 inhibitors. This Review presents a systematic mining of BACE1 inhibitors based on 354 crystal structures of the BACE1 catalytic domain in complex with ligands in the Protein Data Bank. A thorough exploration on the frequency as well as the patterns of residue-ligand interactions enables us to subdivide the ligand binding pocket into 10 subsites and then identify favorable substructures of ligands for each subsite. In addition, it is found that the assembly of subsites with an 8-like shape is responsible to bind all inhibitors and four major ligand binding modes are revealed. Thus, such a systematic survey deepens our understanding of the structural requirements for establishment of BACE1-ligand interactions that determine the affinity of a ligand to BACE1, which is pivotal for structure-based lead optimization and design of novel inhibitors.
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Affiliation(s)
- Hangchen Hu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhaoqiang Chen
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiang Xu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yechun Xu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
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33
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Xu X, Lü P, Wang J, Xu F, Liang L, Wang C, Niu Y, Xu P. Design, synthesis, and biological evaluation of 4‐aminopyrimidine or 4,6‐diaminopyrimidine derivatives as beta amyloid cleaving enzyme‐1 inhibitors. Chem Biol Drug Des 2019; 93:926-933. [DOI: 10.1111/cbdd.13489] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 12/14/2018] [Accepted: 01/09/2019] [Indexed: 02/02/2023]
Affiliation(s)
- Xiufeng Xu
- Department of Medicinal ChemistrySchool of Pharmaceutical SciencesPeking University Health Science Center Beijing China
| | - Peng Lü
- Department of Medicinal ChemistrySchool of Pharmaceutical SciencesPeking University Health Science Center Beijing China
| | - Junjie Wang
- Department of Medicinal ChemistrySchool of Pharmaceutical SciencesPeking University Health Science Center Beijing China
| | - Fengrong Xu
- Department of Medicinal ChemistrySchool of Pharmaceutical SciencesPeking University Health Science Center Beijing China
| | - Lei Liang
- Department of Medicinal ChemistrySchool of Pharmaceutical SciencesPeking University Health Science Center Beijing China
| | - Chao Wang
- Department of Medicinal ChemistrySchool of Pharmaceutical SciencesPeking University Health Science Center Beijing China
| | - Yan Niu
- Department of Medicinal ChemistrySchool of Pharmaceutical SciencesPeking University Health Science Center Beijing China
| | - Ping Xu
- Department of Medicinal ChemistrySchool of Pharmaceutical SciencesPeking University Health Science Center Beijing China
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34
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Kaya S, Gökce H, El-Azab AS, Sert Y, Alanazi MM, Öztürk N, Al-Agamy MHM, Abdel-Aziz AAM. Structural, Spectroscopic, Electronic and Molecular Docking Studies on (11 R
,12 S
)-16-Aminotetracyclo[6.6.2.0 2,7
.0 9,14
]hexadeca-2(7),3,5,9(14),10,12-hexaen-15-ol. ChemistrySelect 2019. [DOI: 10.1002/slct.201803732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Serdal Kaya
- Department of Chemistry; Faculty of Arts and Sciences; Giresun University; 28200 Giresun Turkey
| | - Halil Gökce
- Vocational School of Health Services; Giresun University, 28200; Giresun Turkey
| | - Adel S. El-Azab
- Department of Pharmaceutical Chemistry; College of Pharmacy; King Saud University; 11451 Riyadh Saudi Arabia
- Department of Organic Chemistry; Faculty of Pharmacy; Al-Azhar University; 11884 Cairo Egypt
| | - Yusuf Sert
- Sorgun Vocational School; Bozok University; 66100 Yozgat Turkey
| | - Mohammed M. Alanazi
- Department of Pharmaceutical Chemistry; College of Pharmacy; King Saud University; 11451 Riyadh Saudi Arabia
| | - Nuri Öztürk
- Dereli Vocational School; Giresun University; 28950 Giresun Turkey
| | - Mohamed H. M. Al-Agamy
- Department of Pharmaceutics and Microbiology; College of Pharmacy; King Saud University; Riyadh 11451 Saudi Arabia
| | - Alaa A.-M. Abdel-Aziz
- Department of Pharmaceutical Chemistry; College of Pharmacy; King Saud University; 11451 Riyadh Saudi Arabia
- Department of Medicinal Chemistry; Faculty of Pharmacy; Mansoura University; 35516 Mansoura Egypt
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35
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Schaduangrat N, Prachayasittikul V, Choomwattana S, Wongchitrat P, Phopin K, Suwanjang W, Malik AA, Vincent B, Nantasenamat C. Multidisciplinary approaches for targeting the secretase protein family as a therapeutic route for Alzheimer's disease. Med Res Rev 2019; 39:1730-1778. [PMID: 30628099 DOI: 10.1002/med.21563] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 11/21/2018] [Accepted: 12/24/2018] [Indexed: 12/27/2022]
Abstract
The continual increase of the aging population worldwide renders Alzheimer's disease (AD) a global prime concern. Several attempts have been focused on understanding the intricate complexity of the disease's development along with the on- andgoing search for novel therapeutic strategies. Incapability of existing AD drugs to effectively modulate the pathogenesis or to delay the progression of the disease leads to a shift in the paradigm of AD drug discovery. Efforts aimed at identifying AD drugs have mostly focused on the development of disease-modifying agents in which effects are believed to be long lasting. Of particular note, the secretase enzymes, a group of proteases responsible for the metabolism of the β-amyloid precursor protein (βAPP) and β-amyloid (Aβ) peptides production, have been underlined for their promising therapeutic potential. This review article attempts to comprehensively cover aspects related to the identification and use of drugs targeting the secretase enzymes. Particularly, the roles of secretases in the pathogenesis of AD and their therapeutic modulation are provided herein. Moreover, an overview of the drug development process and the contribution of computational (in silico) approaches for facilitating successful drug discovery are also highlighted along with examples of relevant computational works. Promising chemical scaffolds, inhibitors, and modulators against each class of secretases are also summarized herein. Additionally, multitarget secretase modulators are also taken into consideration in light of the current growing interest in the polypharmacology of complex diseases. Finally, challenging issues and future outlook relevant to the discovery of drugs targeting secretases are also discussed.
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Affiliation(s)
- Nalini Schaduangrat
- Faculty of Medical Technology, Center of Data Mining and Biomedical Informatics, Mahidol University, Bangkok, Thailand
| | - Veda Prachayasittikul
- Faculty of Medical Technology, Center of Data Mining and Biomedical Informatics, Mahidol University, Bangkok, Thailand
| | - Saowapak Choomwattana
- Faculty of Medical Technology, Center of Data Mining and Biomedical Informatics, Mahidol University, Bangkok, Thailand
| | - Prapimpun Wongchitrat
- Faculty of Medical Technology, Center for Research and Innovation, Mahidol University, Bangkok, Thailand
| | - Kamonrat Phopin
- Faculty of Medical Technology, Center for Research and Innovation, Mahidol University, Bangkok, Thailand
| | - Wilasinee Suwanjang
- Faculty of Medical Technology, Center for Research and Innovation, Mahidol University, Bangkok, Thailand
| | - Aijaz Ahmad Malik
- Faculty of Medical Technology, Center of Data Mining and Biomedical Informatics, Mahidol University, Bangkok, Thailand
| | - Bruno Vincent
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand.,Centre National de la Recherche Scientifique, Paris, France
| | - Chanin Nantasenamat
- Faculty of Medical Technology, Center of Data Mining and Biomedical Informatics, Mahidol University, Bangkok, Thailand
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36
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Sharma P, Srivastava P, Seth A, Tripathi PN, Banerjee AG, Shrivastava SK. Comprehensive review of mechanisms of pathogenesis involved in Alzheimer's disease and potential therapeutic strategies. Prog Neurobiol 2018; 174:53-89. [PMID: 30599179 DOI: 10.1016/j.pneurobio.2018.12.006] [Citation(s) in RCA: 202] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 12/04/2018] [Accepted: 12/28/2018] [Indexed: 12/14/2022]
Abstract
AD is a progressive neurodegenerative disorder and a leading cause of dementia in an aging population worldwide. The enormous challenge which AD possesses to global healthcare makes it as urgent as ever for the researchers to develop innovative treatment strategies to fight this disease. An in-depth analysis of the extensive available data associated with the AD is needed for a more comprehensive understanding of underlying molecular mechanisms and pathophysiological pathways associated with the onset and progression of the AD. The currently understood pathological and biochemical manifestations include cholinergic, Aβ, tau, excitotoxicity, oxidative stress, ApoE, CREB signaling pathways, insulin resistance, etc. However, these hypotheses have been criticized with several conflicting reports for their involvement in the disease progression. Several issues need to be addressed such as benefits to cost ratio with cholinesterase therapy, the dilemma of AChE selectivity over BChE, BBB permeability of peptidic BACE-1 inhibitors, hurdles related to the implementation of vaccination and immunization therapy, and clinical failure of candidates related to newly available targets. The present review provides an insight to the different molecular mechanisms involved in the development and progression of the AD and potential therapeutic strategies, enlightening perceptions into structural information of conventional and novel targets along with the successful applications of computational approaches for the design of target-specific inhibitors.
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Affiliation(s)
- Piyoosh Sharma
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Pavan Srivastava
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Ankit Seth
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Prabhash Nath Tripathi
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Anupam G Banerjee
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Sushant K Shrivastava
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India.
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37
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Seong SH, Ha MT, Min BS, Jung HA, Choi JS. Moracin derivatives from Morus Radix as dual BACE1 and cholinesterase inhibitors with antioxidant and anti-glycation capacities. Life Sci 2018; 210:20-28. [DOI: 10.1016/j.lfs.2018.08.060] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 08/22/2018] [Accepted: 08/23/2018] [Indexed: 12/20/2022]
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38
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Graham SE, Leja N, Carlson HA. MixMD Probeview: Robust Binding Site Prediction from Cosolvent Simulations. J Chem Inf Model 2018; 58:1426-1433. [PMID: 29905479 DOI: 10.1021/acs.jcim.8b00265] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mixed-solvent molecular dynamics (MixMD) is a cosolvent simulation technique for identifying binding hotspots and specific favorable interactions on a protein's surface. MixMD studies have the ability to identify these biologically relevant sites by examining the occupancy of the cosolvent over the course of the simulation. However, previous MixMD analysis required a great deal of manual inspection to identify relevant sites. To address this limitation, we have developed MixMD Probeview as a plugin for the freely available, open-source version of the molecular visualization program PyMOL. MixMD Probeview incorporates two analysis procedures: (1) identifying and ranking whole binding sites and (2) identifying and ranking local maxima for each probe type. These functionalities were validated using four common benchmark proteins, including two with both active and allosteric sites. In addition, three different cosolvent procedures were compared to examine the impact of including more than one cosolvent in the simulations. For all systems tested, MixMD Probeview successfully identified known active and allosteric sites based on the total occupancy of neutral probe molecules. As an easy-to-use PyMOL plugin, we expect that MixMD Probeview will facilitate identification and analysis of binding sites from cosolvent simulations performed on a wide range of systems.
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39
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Johansson P, Kaspersson K, Gurrell IK, Bäck E, Eketjäll S, Scott CW, Cebers G, Thorne P, McKenzie MJ, Beaton H, Davey P, Kolmodin K, Holenz J, Duggan ME, Budd Haeberlein S, Bürli RW. Toward β-Secretase-1 Inhibitors with Improved Isoform Selectivity. J Med Chem 2018; 61:3491-3502. [DOI: 10.1021/acs.jmedchem.7b01716] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Patrik Johansson
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, S-43183 Mölndal, Sweden
| | - Karin Kaspersson
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, S-43183 Mölndal, Sweden
| | - Ian K. Gurrell
- Neuroscience, IMED Biotech Unit, AstraZeneca, Cambridge CB21 6GH, U.K
| | - Elisabeth Bäck
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, S-43183 Mölndal, Sweden
| | - Susanna Eketjäll
- Cardiovascular and Metabolic Diseases, IMED Biotech Unit, AstraZeneca, 141 57 Huddinge, Sweden
| | - Clay W. Scott
- Discovery Safety, Drug Safety and Metabolism, IMED Biotech Unit, AstraZeneca, Waltham, Massachusetts 02451, United States
| | - Gvido Cebers
- Neuroscience, IMED Biotech Unit, AstraZeneca, Cambridge CB21 6GH, U.K
| | | | | | | | - Paul Davey
- Oncology Chemistry, IMED Biotech Unit, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | - Jörg Holenz
- Neuroscience, IMED Biotech Unit, AstraZeneca, Cambridge CB21 6GH, U.K
| | - Mark E. Duggan
- Neuroscience, IMED Biotech Unit, AstraZeneca, Cambridge CB21 6GH, U.K
| | | | - Roland W. Bürli
- Neuroscience, IMED Biotech Unit, AstraZeneca, Cambridge CB21 6GH, U.K
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40
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Graham SE, Smith RD, Carlson HA. Predicting Displaceable Water Sites Using Mixed-Solvent Molecular Dynamics. J Chem Inf Model 2018; 58:305-314. [PMID: 29286658 PMCID: PMC6190669 DOI: 10.1021/acs.jcim.7b00268] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Water molecules are an important factor in protein-ligand binding. Upon binding of a ligand with a protein's surface, waters can either be displaced by the ligand or may be conserved and possibly bridge interactions between the protein and ligand. Depending on the specific interactions made by the ligand, displacing waters can yield a gain in binding affinity. The extent to which binding affinity may increase is difficult to predict, as the favorable displacement of a water molecule is dependent on the site-specific interactions made by the water and the potential ligand. Several methods have been developed to predict the location of water sites on a protein's surface, but the majority of methods are not able to take into account both protein dynamics and the interactions made by specific functional groups. Mixed-solvent molecular dynamics (MixMD) is a cosolvent simulation technique that explicitly accounts for the interaction of both water and small molecule probes with a protein's surface, allowing for their direct competition. This method has previously been shown to identify both active and allosteric sites on a protein's surface. Using a test set of eight systems, we have developed a method using MixMD to identify conserved and displaceable water sites. Conserved sites can be determined by an occupancy-based metric to identify sites which are consistently occupied by water even in the presence of probe molecules. Conversely, displaceable water sites can be found by considering the sites which preferentially bind probe molecules. Furthermore, the inclusion of six probe types allows the MixMD method to predict which functional groups are capable of displacing which water sites. The MixMD method consistently identifies sites which are likely to be nondisplaceable and predicts the favorable displacement of water sites that are known to be displaced upon ligand binding.
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Affiliation(s)
- Sarah E. Graham
- Department of Biophysics, College of Pharmacy, University of Michigan, 428 Church St., Ann Arbor, Michigan, 48109-1065
| | - Richard D. Smith
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church St., Ann Arbor, Michigan, 48109-1065
| | - Heather A. Carlson
- Department of Biophysics, College of Pharmacy, University of Michigan, 428 Church St., Ann Arbor, Michigan, 48109-1065
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church St., Ann Arbor, Michigan, 48109-1065
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41
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McGillewie L, Ramesh M, Soliman ME. Sequence, Structural Analysis and Metrics to Define the Unique Dynamic Features of the Flap Regions Among Aspartic Proteases. Protein J 2017; 36:385-396. [PMID: 28762197 DOI: 10.1007/s10930-017-9735-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Aspartic proteases are a class of hydrolytic enzymes that have been implicated in a number of diseases such as HIV, malaria, cancer and Alzheimer's. The flap region of aspartic proteases is a characteristic unique structural feature of these enzymes; and found to have a profound impact on protein overall structure, function and dynamics. Flap dynamics also plays a crucial role in drug binding and drug resistance. Therefore, understanding the structure and dynamic behavior of this flap regions is crucial in the design of potent and selective inhibitors against aspartic proteases. Defining metrics that can describe the flap motion/dynamics has been a challenging topic in literature. This review is the first attempt to compile comprehensive information on sequence, structure, motion and metrics used to assess the dynamics of the flap region of different aspartic proteases in "one pot". We believe that this review would be of critical importance to the researchers from different scientific domains.
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Affiliation(s)
- Lara McGillewie
- Molecular Modelling & Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal (UKZN), Westville, Durban, 4001, South Africa
| | - Muthusamy Ramesh
- Molecular Modelling & Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal (UKZN), Westville, Durban, 4001, South Africa
| | - Mahmoud E Soliman
- Molecular Modelling & Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal (UKZN), Westville, Durban, 4001, South Africa.
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42
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Bertini S, Ghilardi E, Asso V, Minutolo F, Rapposelli S, Digiacomo M, Saccomanni G, Salmaso V, Sturlese M, Moro S, Macchia M, Manera C. Sulfonamido-derivatives of unsubstituted carbazoles as BACE1 inhibitors. Bioorg Med Chem Lett 2017; 27:4812-4816. [DOI: 10.1016/j.bmcl.2017.09.058] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 09/25/2017] [Accepted: 09/27/2017] [Indexed: 12/20/2022]
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Gueto-Tettay C, Martinez-Consuegra A, Zuchniarz J, Gueto-Tettay LR, Drosos-Ramírez JC. A PM7 dynamic residue-ligand interactions energy landscape of the BACE1 inhibitory pathway by hydroxyethylamine compounds. Part I: The flap closure process. J Mol Graph Model 2017; 76:274-288. [PMID: 28746905 DOI: 10.1016/j.jmgm.2017.07.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 07/10/2017] [Accepted: 07/11/2017] [Indexed: 01/08/2023]
Abstract
BACE1 is an enzyme of scientific interest because it participates in the progression of Alzheimer's disease. Hydroxyethylamines (HEAs) are a family of compounds which exhibit inhibitory activity toward BACE1 at a nanomolar level, favorable pharmacokinetic properties and oral bioavailability. The first step in the inhibition of BACE1 by HEAs consists of their entrance into the protease active site and the resultant conformational change in the protein, from Apo to closed form. These two conformations differ in the position of an antiparallel loop (called the flap) which covers the entrance to the catalytic site. For BACE1, closure of this flap is vital to its catalytic activity and to inhibition of the enzyme due to the new interactions thereby formed with the ligand. In the present study a dynamic energy landscape of residue-ligand interaction energies (ReLIE) measured for 112 amino acids in the BACE1 active site and its immediate vicinity during the closure of the flap induced by 8 HEAs of different inhibitory power is presented. A total of 6.272 million ReLIE calculations, based on the PM7 semiempirical method, provided a deep and quantitative view of the first step in the inhibition of the aspartyl protease. The information suggests that residues Asp93, Asp289, Thr292, Thr293, Asn294 and Arg296 are anchor points for the ligand, accounting for approximately 45% of the total protein-ligand interaction. Additionally, flap closure improved the BACE1-HEA interaction by around 25%. Furthermore, the inhibitory activity of HEAs could be related to the capacity of these ligands to form said anchor point interactions and maintain them over time: the lack of some of these anchor interactions delayed flap closure or impeded it completely, or even caused the flap to reopen. The methodology employed here could be used as a tool to evaluate future structural modifications which lead to improvements in the favorability and stability of BACE1-HEA ReLIEs, aiding in the design of better inhibitors.
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Affiliation(s)
- Carlos Gueto-Tettay
- Grupo de Química Bioorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Cartagena, Colombia.
| | - Alejandro Martinez-Consuegra
- Grupo de Química Bioorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Cartagena, Colombia
| | - Joshua Zuchniarz
- Grupo de Química Bioorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Cartagena, Colombia
| | - Luis Roberto Gueto-Tettay
- Grupo de Química Bioorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Cartagena, Colombia
| | - Juan Carlos Drosos-Ramírez
- Grupo de Química Bioorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Cartagena, Colombia.
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Di Pietro O, Juárez-Jiménez J, Muñoz-Torrero D, Laughton CA, Luque FJ. Unveiling a novel transient druggable pocket in BACE-1 through molecular simulations: Conformational analysis and binding mode of multisite inhibitors. PLoS One 2017; 12:e0177683. [PMID: 28505196 PMCID: PMC5432175 DOI: 10.1371/journal.pone.0177683] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 05/01/2017] [Indexed: 12/30/2022] Open
Abstract
The critical role of BACE-1 in the formation of neurotoxic ß-amyloid peptides in the brain makes it an attractive target for an efficacious treatment of Alzheimer's disease. However, the development of clinically useful BACE-1 inhibitors has proven to be extremely challenging. In this study we examine the binding mode of a novel potent inhibitor (compound 1, with IC50 80 nM) designed by synergistic combination of two fragments-huprine and rhein-that individually are endowed with very low activity against BACE-1. Examination of crystal structures reveals no appropriate binding site large enough to accommodate 1. Therefore we have examined the conformational flexibility of BACE-1 through extended molecular dynamics simulations, paying attention to the highly flexible region shaped by loops 8-14, 154-169 and 307-318. The analysis of the protein dynamics, together with studies of pocket druggability, has allowed us to detect the transient formation of a secondary binding site, which contains Arg307 as a key residue for the interaction with small molecules, at the edge of the catalytic cleft. The formation of this druggable "floppy" pocket would enable the binding of multisite inhibitors targeting both catalytic and secondary sites. Molecular dynamics simulations of BACE-1 bound to huprine-rhein hybrid compounds support the feasibility of this hypothesis. The results provide a basis to explain the high inhibitory potency of the two enantiomeric forms of 1, together with the large dependence on the length of the oligomethylenic linker. Furthermore, the multisite hypothesis has allowed us to rationalize the inhibitory potency of a series of tacrine-chromene hybrid compounds, specifically regarding the apparent lack of sensitivity of the inhibition constant to the chemical modifications introduced in the chromene unit. Overall, these findings pave the way for the exploration of novel functionalities in the design of optimized BACE-1 multisite inhibitors.
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Affiliation(s)
- Ornella Di Pietro
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine, University of Barcelona, Barcelona, Spain
| | - Jordi Juárez-Jiménez
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine, Campus Torribera, University of Barcelona, Santa Coloma de Gramenet, Spain
| | - Diego Muñoz-Torrero
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine, University of Barcelona, Barcelona, Spain
| | - Charles A. Laughton
- School of Pharmacy and Centre for Biomolecular Sciences, University Park, Nottingham, United Kingdom
- * E-mail: (CAL); (FJL)
| | - F. Javier Luque
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine, Campus Torribera, University of Barcelona, Santa Coloma de Gramenet, Spain
- * E-mail: (CAL); (FJL)
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Keränen H, Pérez-Benito L, Ciordia M, Delgado F, Steinbrecher TB, Oehlrich D, van Vlijmen HWT, Trabanco AA, Tresadern G. Acylguanidine Beta Secretase 1 Inhibitors: A Combined Experimental and Free Energy Perturbation Study. J Chem Theory Comput 2017; 13:1439-1453. [PMID: 28103438 DOI: 10.1021/acs.jctc.6b01141] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
A series of acylguanidine beta secretase 1 (BACE1) inhibitors with modified scaffold and P3 pocket substituent was synthesized and studied with free energy perturbation (FEP) calculations. The resulting molecules showed potencies in enzymatic BACE1 inhibition assays up to 1 nM. The correlation between the predicted activity from the FEP calculations and the experimental activity was good for the P3 pocket substituents. The average mean unsigned error (MUE) between prediction and experiment was 0.68 ± 0.17 kcal/mol for the default 5 ns lambda window simulation time improving to 0.35 ± 0.13 kcal/mol for 40 ns. FEP calculations for the P2' pocket substituents on the same acylguanidine scaffold also showed good agreement with experiment and the results remained stable with repeated simulations and increased simulation time. It proved more difficult to use FEP calculations to study the scaffold modification from increasing 5 to 6 and 7 membered-rings. Although prediction and experiment were in agreement for short 2 ns simulations, as the simulation time increased the results diverged. This was improved by the use of a newly developed "Core Hopping FEP+" approach, which also showed improved stability in repeat calculations. The origins of these differences along with the value of repeat and longer simulation times are discussed. This work provides a further example of the use of FEP as a computational tool for molecular design.
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Affiliation(s)
- Henrik Keränen
- Computational Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V. , Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Laura Pérez-Benito
- Laboratori de Medicina Computacional Unitat de Bioestadistica, Facultat de Medicina, Universitat Autonoma de Barcelona , 08193, Bellaterra, Spain.,Computational Chemistry, Janssen Research and Development, Janssen-Cilag , c/ Jarama 75A, 45007, Toledo, Spain
| | - Myriam Ciordia
- Neuroscience Medicinal Chemistry, Janssen Research and Development, Janssen-Cilag , c/ Jarama 75A, 45007, Toledo, Spain
| | - Francisca Delgado
- Neuroscience Medicinal Chemistry, Janssen Research and Development, Janssen-Cilag , c/ Jarama 75A, 45007, Toledo, Spain
| | | | - Daniel Oehlrich
- Neuroscience Medicinal Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V. , Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Herman W T van Vlijmen
- Computational Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V. , Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Andrés A Trabanco
- Neuroscience Medicinal Chemistry, Janssen Research and Development, Janssen-Cilag , c/ Jarama 75A, 45007, Toledo, Spain
| | - Gary Tresadern
- Computational Chemistry, Janssen Research and Development, Janssen-Cilag , c/ Jarama 75A, 45007, Toledo, Spain
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46
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Kocak A, Erol I, Yildiz M, Can H. Computational insights into the protonation states of catalytic dyad in BACE1–acyl guanidine based inhibitor complex. J Mol Graph Model 2016; 70:226-235. [DOI: 10.1016/j.jmgm.2016.10.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 10/10/2016] [Accepted: 10/14/2016] [Indexed: 12/13/2022]
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47
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Gueto-Tettay C, Zuchniarz J, Fortich-Seca Y, Gueto-Tettay LR, Drosos-Ramirez JC. A molecular dynamics study of the BACE1 conformational change from Apo to closed form induced by hydroxyethylamine derived compounds. J Mol Graph Model 2016; 70:181-195. [PMID: 27750187 DOI: 10.1016/j.jmgm.2016.10.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 10/05/2016] [Accepted: 10/06/2016] [Indexed: 12/11/2022]
Abstract
BACE1 is an aspartyl protease which is a therapeutic target for Alzheimer's disease (AD) because of its participation in the rate-limiting step in the production of Aβ-peptide, the accumulation of which produces senile plaques and, in turn, the neurodegenerative effects associated with AD. The active site of this protease is composed in part by two aspartic residues (Asp93 and Asp289). Additionally, the catalytic site has been found to be covered by an antiparallel hairpin loop called the flap. The dynamics of this flap are fundamental to the catalytic function of the enzyme. When BACE1 is inactive (Apo), the flap adopts an open conformation, allowing a substrate or inhibitor to access the active site. Subsequent interaction with the ligand induces flap closure and the stabilization of the macromolecular complex. Further, the protonation state of the aspartic dyad is affected by the chemical nature of the species entering the active site, so that appropriate selection of protonation states for the ligand and the catalytic residues will permit the elucidation of the inhibitory pathway for BACE1. In the present study, comparative analysis of different combinations of protonation states for the BACE1-hydroxyethylamine (HEA) system is reported. HEAs are potent inhibitors of BACE1 with favorable pharmacological and kinetic properties, as well as oral bioavailability. The results of Molecular Dynamics (MD) simulations and population density calculations using 8 different parameters demonstrate that the LnAsp289 configuration (HEA with a neutral amine and the Asp289 residue protonated) is the only one which permits the expected conformational change in BACE1, from apo to closed form, after flap closure. Additionally, differences in their capacities to establish and maintain interactions with residues such as Asp93, Gly95, Thr133, Asp289, Gly291, and Asn294 during this step allow differentiation among the inhibitory activities of the HEAs. The results and methodology here reported will serve to elucidate the inhibitory pathway of other families of compounds that act as BACE1 inhibitors, as well as the design of better leader compounds for the treatment of AD.
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Affiliation(s)
- Carlos Gueto-Tettay
- Grupo de Química Bioorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Colombia
| | - Joshua Zuchniarz
- Grupo de Química Bioorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Colombia
| | - Yeyson Fortich-Seca
- Grupo de Química Bioorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Colombia
| | - Luis Roberto Gueto-Tettay
- Grupo de Química Bioorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Colombia
| | - Juan Carlos Drosos-Ramirez
- Grupo de Química Bioorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Colombia.
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48
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Multi-target screening mines hesperidin as a multi-potent inhibitor: Implication in Alzheimer's disease therapeutics. Eur J Med Chem 2016; 121:810-822. [DOI: 10.1016/j.ejmech.2016.03.057] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 03/09/2016] [Accepted: 03/20/2016] [Indexed: 01/09/2023]
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49
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Sabbah DA, Zhong HA. Modeling the protonation states of β-secretase binding pocket by molecular dynamics simulations and docking studies. J Mol Graph Model 2016; 68:206-215. [DOI: 10.1016/j.jmgm.2016.07.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 07/06/2016] [Accepted: 07/17/2016] [Indexed: 01/12/2023]
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50
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Estrada M, Pérez C, Soriano E, Laurini E, Romano M, Pricl S, Morales-García JA, Pérez-Castillo A, Rodríguez-Franco MI. New neurogenic lipoic-based hybrids as innovative Alzheimer's drugs with σ-1 agonism and β-secretase inhibition. Future Med Chem 2016; 8:1191-207. [PMID: 27402296 DOI: 10.4155/fmc-2016-0036] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Neurogenic agents emerge as innovative drugs for the treatment of Alzheimer's disease (AD), whose pathological complexity suggests strengthening research in the multi-target directed ligands strategy. RESULTS By combining the lipoic acid structure with N-benzylpiperidine or N,N-dibenzyl(N-methyl)amine fragments, new multi-target directed ligands were obtained that act at three relevant targets in AD: σ-1 receptor (σ1R), β-secretase-1 (BACE1) and acetylcholinesterase (AChE). Moreover, they show potent neurogenic properties, good antioxidant capacity and favorable CNS permeability. Molecular modeling studies on AChE, σ1R and BACE1 highlight relevant drug-protein interactions that may contribute to the development of new disease-modifying drugs. CONCLUSION New lipoic-based σ1 agonists endowed with neurogenic, antioxidant, cholinergic and amyloid β-peptide-reducing properties have been discovered for the potential treatment of AD.
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Affiliation(s)
- Martín Estrada
- Instituto de Química Médica (IQM-CSIC), C/Juan de la Cierva 3, 28006-Madrid, Spain
| | - Concepción Pérez
- Instituto de Química Médica (IQM-CSIC), C/Juan de la Cierva 3, 28006-Madrid, Spain
| | - Elena Soriano
- Instituto de Química Orgánica General (IQOG-CSIC), C/Juan de la Cierva 3, 28006-Madrid, Spain
| | - Erik Laurini
- Molecular Simulation Engineering (MOSE) Laboratory, DEA, Piazzale Europa 1, University of Trieste, 34127 Trieste, Italy
| | - Maurizio Romano
- Department of Life Sciences, University of Trieste, Via A. Valerio 28, 34127 - Trieste, Italy
| | - Sabrina Pricl
- Molecular Simulation Engineering (MOSE) Laboratory, DEA, Piazzale Europa 1, University of Trieste, 34127 Trieste, Italy
- National Interuniversity Consortium for Material Science & Technology (INSTM), Research Unit MOSE-DEA, University of Trieste, Trieste, Italy
| | - José A Morales-García
- Instituto de Investigaciones Biomédicas "Alberto Sols" (IIB-CSIC), C/Arturo Duperier 4, 28029-Madrid, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), C/Valderrebollo 5, 28031-Madrid, Spain
| | - Ana Pérez-Castillo
- Instituto de Investigaciones Biomédicas "Alberto Sols" (IIB-CSIC), C/Arturo Duperier 4, 28029-Madrid, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), C/Valderrebollo 5, 28031-Madrid, Spain
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