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Hsieh CJ, Giannakoulias S, Petersson EJ, Mach RH. Computational Chemistry for the Identification of Lead Compounds for Radiotracer Development. Pharmaceuticals (Basel) 2023; 16:317. [PMID: 37259459 PMCID: PMC9964981 DOI: 10.3390/ph16020317] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 11/19/2023] Open
Abstract
The use of computer-aided drug design (CADD) for the identification of lead compounds in radiotracer development is steadily increasing. Traditional CADD methods, such as structure-based and ligand-based virtual screening and optimization, have been successfully utilized in many drug discovery programs and are highlighted throughout this review. First, we discuss the use of virtual screening for hit identification at the beginning of drug discovery programs. This is followed by an analysis of how the hits derived from virtual screening can be filtered and culled to highly probable candidates to test in in vitro assays. We then illustrate how CADD can be used to optimize the potency of experimentally validated hit compounds from virtual screening for use in positron emission tomography (PET). Finally, we conclude with a survey of the newest techniques in CADD employing machine learning (ML).
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Affiliation(s)
- Chia-Ju Hsieh
- Division of Nuclear Medicine and Clinical Molecular Imaging, Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sam Giannakoulias
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - E. James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Robert H. Mach
- Division of Nuclear Medicine and Clinical Molecular Imaging, Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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2
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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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3
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King E, Aitchison E, Li H, Luo R. Recent Developments in Free Energy Calculations for Drug Discovery. Front Mol Biosci 2021; 8:712085. [PMID: 34458321 PMCID: PMC8387144 DOI: 10.3389/fmolb.2021.712085] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/27/2021] [Indexed: 01/11/2023] Open
Abstract
The grand challenge in structure-based drug design is achieving accurate prediction of binding free energies. Molecular dynamics (MD) simulations enable modeling of conformational changes critical to the binding process, leading to calculation of thermodynamic quantities involved in estimation of binding affinities. With recent advancements in computing capability and predictive accuracy, MD based virtual screening has progressed from the domain of theoretical attempts to real application in drug development. Approaches including the Molecular Mechanics Poisson Boltzmann Surface Area (MM-PBSA), Linear Interaction Energy (LIE), and alchemical methods have been broadly applied to model molecular recognition for drug discovery and lead optimization. Here we review the varied methodology of these approaches, developments enhancing simulation efficiency and reliability, remaining challenges hindering predictive performance, and applications to problems in the fields of medicine and biochemistry.
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Affiliation(s)
- Edward King
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | - Erick Aitchison
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | - Han Li
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA, United States
| | - Ray Luo
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA, United States
- Department of Materials Science and Engineering, University of California, Irvine, CA, United States
- Department of Biomedical Engineering, University of California, Irvine, CA, United States
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4
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Motoyama M, Doan TH, Hibner-Kulicka P, Otake R, Lukarska M, Lohier JF, Ozawa K, Nanbu S, Alayrac C, Suzuki Y, Witulski B. Synthesis and Structure-Photophysics Evaluation of 2-N-Amino-quinazolines: Small Molecule Fluorophores for Solution and Solid State. Chem Asian J 2021; 16:2087-2099. [PMID: 34107175 DOI: 10.1002/asia.202100534] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/08/2021] [Indexed: 11/12/2022]
Abstract
2-N-aminoquinazolines were prepared by consecutive SN Ar functionalization. X-ray structures display the nitrogen lone pair of the 2-N-morpholino group in conjugation with the electron deficient quinazoline core and thus representing electronic push-pull systems. 2-N-aminoquinazolines show a positive solvatochromism and are fluorescent in solution and in solid state with quantum yields up to 0.73. Increase in electron donor strength of the 2-amino substituent causes a red-shift of the intramolecular charge transfer (ICT) band (300-400 nm); whereas the photoluminescence emission maxima (350-450 nm) is also red-shifted significantly along with an enhancement in photoluminescence efficiency. HOMO-LUMO energies were estimated by a combination of electrochemical and photophysical methods and correlate well to those obtained by computational methods. ICT properties are theoretically attributed to an excitation to Rydberg-MO in SAC-CI method, which can be interpreted as n-π* excitation. 7-Amino-2-N-morpholino-4-methoxyquinazoline responds to acidic conditions with significant increases in photoluminescence intensity revealing a new turn-on/off fluorescence probe.
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Affiliation(s)
- Miho Motoyama
- Department of Life and Material Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioicho, Chiyodaku, 102-8554, Tokyo, Japan
| | - Thu-Hong Doan
- Laboratoire de Chimie Moléculaire et Thio-organique, CNRS UMR 6507, ENSICAEN & UNICAEN, Normandie Univ., 6 Bvd Maréchal Juin, 14050, Caen, France
| | - Paulina Hibner-Kulicka
- Laboratoire de Chimie Moléculaire et Thio-organique, CNRS UMR 6507, ENSICAEN & UNICAEN, Normandie Univ., 6 Bvd Maréchal Juin, 14050, Caen, France
| | - Ryo Otake
- Department of Life and Material Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioicho, Chiyodaku, 102-8554, Tokyo, Japan
| | - Malgorzata Lukarska
- Laboratoire de Chimie Moléculaire et Thio-organique, CNRS UMR 6507, ENSICAEN & UNICAEN, Normandie Univ., 6 Bvd Maréchal Juin, 14050, Caen, France
| | - Jean-Francois Lohier
- Laboratoire de Chimie Moléculaire et Thio-organique, CNRS UMR 6507, ENSICAEN & UNICAEN, Normandie Univ., 6 Bvd Maréchal Juin, 14050, Caen, France
| | - Kota Ozawa
- Department of Life and Material Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioicho, Chiyodaku, 102-8554, Tokyo, Japan
| | - Shinkoh Nanbu
- Department of Life and Material Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioicho, Chiyodaku, 102-8554, Tokyo, Japan
| | - Carole Alayrac
- Laboratoire de Chimie Moléculaire et Thio-organique, CNRS UMR 6507, ENSICAEN & UNICAEN, Normandie Univ., 6 Bvd Maréchal Juin, 14050, Caen, France
| | - Yumiko Suzuki
- Department of Life and Material Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioicho, Chiyodaku, 102-8554, Tokyo, Japan
| | - Bernhard Witulski
- Laboratoire de Chimie Moléculaire et Thio-organique, CNRS UMR 6507, ENSICAEN & UNICAEN, Normandie Univ., 6 Bvd Maréchal Juin, 14050, Caen, France
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5
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Mei J, Yang H, Sun B, Liu C, Ai H. Small-Molecule Targeted Aβ 42 Aggregate Degradation: Negatively Charged Small Molecules Are More Promising than the Neutral Ones. ACS Chem Neurosci 2021; 12:1197-1209. [PMID: 33687193 DOI: 10.1021/acschemneuro.1c00047] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Heavy evidence has confirmed that Aβ42 oligomers are the most neurotoxic aggregates and play a critical role in the occurrence and development of Alzheimer's disease by causing functional neuron death, cognitive damage, and dementia. Disordered Aβ42 oligomers are challenging therapeutic targets, and no drug is currently in clinical use that modifies the properties of their monomeric states. Here, a negatively charged molecule (ER), rather than the neutral TS1 one, is identified by a molecular dynamics simulation method to be more capable of binding and sequestering the intrinsically disordered amyloid-β peptide Aβ42 in its soluble pentameric state as well as its monomeric components. Results reveal that the ERs interact with Aβ and inhibit the primary nucleation pathways in its aggregation process in entropic expansion mechanism for both Aβ42 and Aβ40 oligomers but with opposite characteristics of hydrophobic surface area (HSA). The interaction between Aβ42 oligomer and either charged ER or neutral TS1/TS0 characterizes decreased HSA, and the decrease in ER-involved case is highly visible, consistent with the observations from in silico and in vitro studies. By contrast, the presence of these inhibitors causes the HSA of Aβ40 oligomer to change undetectably and there is even a bit of increase in the histidine isomerized Aβ40 oligomer. The HSA distinction between Aβ42 and Aβ40 oligomer is possibly derived from the different effects of M35-inhibitor interaction, which is analogous to the effect of M35 oxidation. In comparison with the neutral TS1/TS0 inhibitors, ER is more prone to bind the residues located in the central (β1) and C-terminal (β2) regions of Aβ42 peptide, two key nucleation regions for Aβ intramolecular folding, intermolecular aggregation, and assembly. Notably, ER can strongly bind the charged residues, such as K16, K28, D23, to greatly disturb the potential stabilizer (e.g., salt-bridge, etc.) in metastable Aβ42 oligomers and protofibrils. These results illustrate the strategy of overcoming Alzheimer's disease from inhibiting its early stage Aβ aggregation with two kinds of small molecules to alter their behavior for therapeutic purposes and strongly recommend paying more attention to the engineering and development of negatively charged inhibitors, the long-term underappreciated ones, targeting the early stage Aβ aggregates.
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Affiliation(s)
- Jinfei Mei
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Huijuan Yang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Bo Sun
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Chengqiang Liu
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Hongqi Ai
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
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Gong Y, Zhan C, Zou Y, Qian Z, Wei G, Zhang Q. Serotonin and Melatonin Show Different Modes of Action on Aβ 42 Protofibril Destabilization. ACS Chem Neurosci 2021; 12:799-809. [PMID: 33533252 DOI: 10.1021/acschemneuro.1c00038] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Alzheimer's disease (AD) is associated with the aberrant self-assembly of amyloid-β (Aβ) protein into fibrillar deposits. The disaggregation of Aβ fibril is believed as one of the major therapeutic strategies for treating AD. Previous experimental studies reported that serotonin (Ser), one of the indoleamine neurotransmitters, and its derivative melatonin (Mel) are able to disassemble preformed Aβ fibrils. However, the fibril-disruption mechanisms are unclear. As the first step to understand the underlying mechanism, we investigated the interactions of Ser and Mel molecules with the LS-shaped Aβ42 protofibril by performing a total of nine individual 500 ns all-atom molecular dynamics (MD) simulations. The simulations demonstrate that both Ser and Mel molecules disrupt the local β-sheet structure, destroy the salt bridges between K28 side chain and A42 COO-, and consequently destabilize the global structure of Aβ42 protofibril. The Mel molecule exhibits a greater binding capacity than the Ser molecule. Intriguingly, we find that Ser and Mel molecules destabilize Aβ42 protofibril through different modes of action. Ser preferentially binds with the aromatic residues in the N-terminal region through π-π stacking interactions, while Mel binds not only with the N-terminal aromatic residues but also with the C-terminal hydrophobic residues via π-π and hydrophobic interactions. This work reveals the disruptive mechanisms of Aβ42 protofibril by Ser and Mel molecules and provides useful information for designing drug candidates against AD.
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Affiliation(s)
- Yehong Gong
- College of Physical Education and Training, Shanghai University of Sport, 399 Chang Hai Road, Shanghai 200438, People’s Republic of China
| | - Chendi Zhan
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People’s Republic of China
| | - Yu Zou
- Department Sport and Exercise Science, College of Education, Zhejiang University, 148 Tianmenshan Road, Hangzhou, 310007 Zhejiang People’s Republic of China
| | - Zhenyu Qian
- Key Laboratory of Exercise and Health Sciences (Ministry of Education) and School of Kinesiology, Shanghai University of Sport, 399 Chang Hai Road, Shanghai 200438, People’s Republic of China
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People’s Republic of China
| | - Qingwen Zhang
- College of Physical Education and Training, Shanghai University of Sport, 399 Chang Hai Road, Shanghai 200438, People’s Republic of China
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7
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Kaur A, Goyal D, Goyal B. An α-helix mimetic oligopyridylamide, ADH-31, modulates Aβ 42 monomer aggregation and destabilizes protofibril structures: insights from molecular dynamics simulations. Phys Chem Chem Phys 2020; 22:28055-28073. [PMID: 33289734 DOI: 10.1039/d0cp04672h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Alzheimer's disease (AD), an epidemic growing worldwide due to no effective medical aid available in the market, is a neurological disorder. AD is known to be directly associated with the toxicity of amyloid-β (Aβ) aggregates. In search of potent inhibitors of Aβ aggregation, Hamilton and co-workers reported an α-helix mimetic, ADH-31, which acts as a powerful antagonist of Aβ42 aggregation. To identify the key interactions between protein-ligand complexes and to gain insights into the inhibitory mechanism of ADH-31 against Aβ42 aggregation, molecular dynamics (MD) simulations were performed in the present study. The MD simulations highlighted that ADH-31 showed distinct binding capabilities with residues spanning from the N-terminal to the central hydrophobic core (CHC) region of Aβ42 and restricted the conformational transition of the helix-rich structure of Aβ42 into another form of secondary structures (coil/turn/β-sheet). Hydrophobic contacts, hydrogen bonding and π-π interaction contribute to the strong binding between ADH-31 and Aβ42 monomer. The Dictionary of Secondary Structure of Proteins (DSSP) analysis highlighted that the probability of helical content increases from 38.5% to 50.2% and the turn content reduces from 14.7% to 6.2% with almost complete loss of the β-sheet structure (4.5% to 0%) in the Aβ42 monomer + ADH-31 complex. The per-residue binding free energy analysis demonstrated that Arg5, Tyr10, His14, Gln15, Lys16, Val18, Phe19 and Lys28 residues of Aβ42 are responsible for the favourable binding free energy in Aβ42 monomer + ADH-31 complex, which is consistent with the 2D HSQC NMR of the Aβ42 monomer that depicted a change in the chemical shift of residues spanning from Glu11 to Phe20 in the presence of ADH-31. The MD simulations highlighted the prevention of sampling of amyloidogenic β-strand conformations in Aβ42 trimer in the presence of ADH-31 as well as the ability of ADH-31 to destabilize Aβ42 trimer and protofibril structures. The lower binding affinity between Aβ42 trimer chains in the presence of ADH-31 highlights the destabilization of the Aβ42 trimer structure. Overall, MD results highlighted that ADH-31 inhibited Aβ42 aggregation by constraining Aβ peptides into helical conformation and destabilized Aβ42 trimer as well as protofibril structures. The present study provides a theoretical insight into the atomic level details of the inhibitory mechanism of ADH-31 against Aβ42 aggregation as well as protofibril destabilization and could be implemented in the structure-based drug design of potent therapeutic agents for AD.
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Affiliation(s)
- Anupamjeet Kaur
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib-140406, Punjab, India.
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8
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Wang Z, Li H, Peng Z, Wang Z, Wang Y, Lu P. Preparation and photophysical properties of quinazoline-based fluorophores. RSC Adv 2020; 10:30297-30303. [PMID: 35516009 PMCID: PMC9056281 DOI: 10.1039/d0ra05701k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/07/2020] [Indexed: 12/15/2022] Open
Abstract
The donor-acceptor design is a classic method of synthesizing new fluorescent molecules. In this study, a series of new fluorescent compounds (1-10) were synthesized based on 2-(3,5-bis(trifluoromethyl)phenyl)-quinazoline acceptor and various amino donors. The fluorescent emissions of 1-10 cover the spectrum from 414 nm to 597 nm in cyclohexane solutions with various amino donors on 4- or 7-positions of quinazoline. Ultimately, compounds 1 and 2 presented the highest photoluminescence quantum yield (QY) over 80%, while compound 10 provided the largest Stokes shift (161 nm) in cyclohexane. Most of them have strong emissions in aggregated states such as in nanoparticles, in powders, in crystals and in films. Mechanochromic properties were observed for compounds 1, 2, 4 and 7. Furthermore, blue OLEDs were fabricated by using compound 2 or 7 as the active layer.
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Affiliation(s)
- Zhichao Wang
- Department of Chemistry, Zhejiang University Hangzhou 310027 P. R. China
| | - Hanjie Li
- Department of Chemistry, Zhejiang University Hangzhou 310027 P. R. China
| | - Zhixing Peng
- Department of Chemistry, Zhejiang University Hangzhou 310027 P. R. China
| | - Zaibin Wang
- Department of Chemistry, Zhejiang University Hangzhou 310027 P. R. China
| | - Yanguang Wang
- Department of Chemistry, Zhejiang University Hangzhou 310027 P. R. China
| | - Ping Lu
- Department of Chemistry, Zhejiang University Hangzhou 310027 P. R. China
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9
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Kaur A, Kaur A, Goyal D, Goyal B. How Does the Mono-Triazole Derivative Modulate Aβ 42 Aggregation and Disrupt a Protofibril Structure: Insights from Molecular Dynamics Simulations. ACS OMEGA 2020; 5:15606-15619. [PMID: 32637837 PMCID: PMC7331201 DOI: 10.1021/acsomega.0c01825] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 06/08/2020] [Indexed: 05/31/2023]
Abstract
Clinical studies have identified that abnormal self-assembly of amyloid-β (Aβ) peptide into toxic fibrillar aggregates is associated with the pathology of Alzheimer's disease (AD). The most acceptable therapeutic approach to stop the progression of AD is to inhibit the formation of β-sheet-rich structures. Recently, we designed and evaluated a series of novel mono-triazole derivatives 4(a-x), where compound 4v was identified as the most potent inhibitor of Aβ42 aggregation and disaggregates preformed Aβ42 fibrils significantly. Moreover, 4v strongly averts the Cu2+-induced Aβ42 aggregation and disaggregates the preformed Cu2+-induced Aβ42 fibrils, halts the generation of reactive oxygen species, and shows neuroprotective effects in SH-SY5Y cells. However, the underlying molecular mechanism of inhibition of Aβ42 aggregation by 4v and disaggregation of preformed Aβ42 fibrils remains obscure. In this work, molecular dynamics (MD) simulations have been performed to explore the conformational ensemble of the Aβ42 monomer and a pentameric protofibril structure of Aβ42 in the presence of 4v. The MD simulations highlighted that 4v binds preferentially at the central hydrophobic core region of the Aβ42 monomer and chains D and E of the Aβ42 protofibril. The dictionary of secondary structure of proteins analysis indicated that 4v retards the conformational conversion of the helix-rich structure of the Aβ42 monomer into the aggregation-prone β-sheet conformation. The binding free energy calculated by the molecular mechanics Poisson-Boltzmann surface area method revealed an energetically favorable process with ΔG binding = -44.9 ± 3.3 kcal/mol for the Aβ42 monomer-4v complex. The free energy landscape analysis highlighted that the Aβ42 monomer-4v complex sampled conformations with significantly higher helical contents (35 and 49%) as compared to the Aβ42 monomer alone (17%). Compound 4v displayed hydrogen bonding with Gly37 (chain E) and π-π interactions with Phe19 (chain D) of the Aβ42 protofibril. Further, the per-residue binding free energy analysis also highlighted that Phe19 (chain D) and Gly37 (chain E) of the Aβ42 protofibril showed the maximum contribution in the binding free energy. The decreased binding affinity and residue-residue contacts between chains D and E of the Aβ42 protofibril in the presence of 4v indicate destabilization of the Aβ42 protofibril structure. Overall, the structural information obtained through MD simulations indicated that 4v stabilizes the native helical conformation of the Aβ42 monomer and persuades a destabilization in the protofibril structure of Aβ42. The results of the study will be useful in the rational design of potent inhibitors against amyloid aggregation.
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Affiliation(s)
- Amandeep Kaur
- Department
of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib 140406, Punjab, India
| | - Anupamjeet Kaur
- Department
of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib 140406, Punjab, India
| | - Deepti Goyal
- Department
of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib 140406, Punjab, India
| | - Bhupesh Goyal
- School
of Chemistry & Biochemistry, Thapar
Institute of Engineering & Technology, Patiala 147004, Punjab, India
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10
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Gancar M, Ho K, Mohid SA, Thai NQ, Bednarikova Z, Nguyen HL, Bhunia A, Nepovimova E, Li MS, Gazova Z. 7-Methoxytacrine and 2-Aminobenzothiazole Heterodimers: Structure-Mechanism Relationship of Amyloid Inhibitors Based on Rational Design. ACS Chem Neurosci 2020; 11:715-729. [PMID: 32011847 DOI: 10.1021/acschemneuro.9b00419] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The formation and accumulation of amyloid aggregates are the phenomena that accompany amyloidoses, which are currently untreatable and include Alzheimer's and Parkinson's diseases, diabetes mellitus, non-neuropathic lysozyme systemic amyloidosis, and others. One of the very promising therapeutic approaches seems to be an inhibition of amyloid formation and/or clearance of amyloid aggregates. Small molecules have a great potential to interfere with amyloid fibrillation of peptides and polypeptides, which can be improved by connection of cyclic structures into single multicyclic molecules and their dimerization. In our study, we focused on heterodimers consisting of 7-methoxytacrine (7-MEOTA) and 2-aminobenzothiazole (BTZ) parent molecules connected by an aliphatic linker. Using in vitro and in silico methods, we investigated the ability of studied compounds to inhibit the amyloid aggregation of hen egg white lysozyme. Heterodimerization led to significant improvement of inhibitory activity compared to that of the parent molecules. The efficiency of the heterodimers varied; the most effective inhibitor contained the longest linker, eight carbons long. We suggest that binding of a heterodimer to a lysozyme blocks the interaction between the β-domain and C-helix region essential for the formation of amyloid cross-β structure. Elongation of the linker ultimately enhances the compound's ability to prevent this interaction by allowing the BTZ part of the heterodimer to bind more effectively, increasing the compound's binding affinity, and also by greater steric obstruction. This study represents an important contribution to the recent rational design of potential lead small molecules with anti-amyloid properties, and the heterodimers studied are prospective candidates for the treatment of systemic lysozyme amyloidosis and other amyloid-related diseases.
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Affiliation(s)
- Miroslav Gancar
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 040 01 Kosice, Slovakia
| | - Kiet Ho
- Life Science Lab, Institute of Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City 700000, Vietnam
| | - Sk. Abdul Mohid
- Department of Biophysics, Bose Institute, Centenary Campus, P-1/12, Ghose Bagan, CIT Road Scheme VIIM, West Bengal 700054, Kolkata, India
| | - Nguyen Quoc Thai
- Dong Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh City 700000, Dong Thap, Vietnam
| | - Zuzana Bednarikova
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 040 01 Kosice, Slovakia
| | - H. Linh Nguyen
- Life Science Lab, Institute of Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City 700000, Vietnam
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, Centenary Campus, P-1/12, Ghose Bagan, CIT Road Scheme VIIM, West Bengal 700054, Kolkata, India
| | - Eugenie Nepovimova
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Rokitanskeho 62, 500 03 Hradec Kralove, Czech Republic
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Zuzana Gazova
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 040 01 Kosice, Slovakia
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Xing X, Liu C, Ali A, Kang B, Li P, Ai H. Novel Disassembly Mechanisms of Sigmoid Aβ 42 Protofibrils by Introduced Neutral and Charged Drug Molecules. ACS Chem Neurosci 2020; 11:45-56. [PMID: 31697060 DOI: 10.1021/acschemneuro.9b00550] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Alzheimer's disease (AD) is characterized by fibrillar deposits of amyloid-β (Aβ) peptides and neurofibrillary tangles of Tau proteins. Aβ peptides are composed of 37-49 residues, among which the Aβ42 isoform is particularly toxic and aggregation-prone and is enriched in the plaques of AD brains and thus considered central to the development of AD. Therefore, disaggregation and disruption provide potential therapeutic approaches to reduce, inhibit, and even reverse Aβ aggregation. Here we capture the atomic-level details of the interactions between sigmoid Aβ42 fibril 2MXU or 5KK3 and either natural tanshinone compounds TS1 or TS0 or negatively charged ER, proposing two unprecedented disassembly mechanisms. Natural TS1 or TS0 prefers to insert into the cavity together with part at the surface of the 2MXU to open up the mouth and twist the conformation, destroying the ordered growth of subsequent monomers along the fibril axis. For the more compact two-fold 5KK3 , attachment of TS1 or TS0 at the surface including some inserted in cavity results in the separation of the two folds. In the two sigmoid fibril systems, it is no longer applicable for the routine criteria to assess Aβ42 fibril disassembly by introduction of these drugs, such as either reduced H-bond number, decreased β-sheet contents, or both. ER, like-charged to Aβ42 fibril, is especially exceptional, and departs utterly from the neutral ones to disassemble Aβ42 fibril. Besides the inapplicable routine criteria, positive binding energy between ER and Aβ42 fibril also deviates from the hypotheses of "ligands exhibiting greater affinity for the β-amyloid peptide are effective at altering its aggregation and inhibiting cell toxicity" ( Cairo et al. , Biochemistry 2002 , 41 , 8620 - 8629 ) but results in stronger disassembly effect on the two kinds of sigmoid Aβ42 fibrils than neutral TS0 or TS1. The disassembly power of charged ER molecules derives from its stronger deformation ability to the conformation of Aβ42 fibril than the neutral ones, twisting the one-fold 2MXU into tapered-shape and separating two-fold 5KK3 in two parts further, which is in great agreement with experimental observations ( Irwin et al. Biomacromolecules 2013 , 14 ( 1 ), 264 - 274 ). The unusual disassembly mechanisms fill the gaps and offer an alternative direction in engineering new inhibitors to treat AD.
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Affiliation(s)
- Xiaofeng Xing
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, PR China
| | - Chengqiang Liu
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, PR China
| | - Aqsa Ali
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, PR China
| | - Baotao Kang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, PR China
| | - Ping Li
- Key Laboratory of Life-Organic Analysis, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, China
| | - Hongqi Ai
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, PR China
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Kaur A, Shuaib S, Goyal D, Goyal B. Interactions of a multifunctional di-triazole derivative with Alzheimer's Aβ42monomer and Aβ42protofibril: a systematic molecular dynamics study. Phys Chem Chem Phys 2020; 22:1543-1556. [DOI: 10.1039/c9cp04775a] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The molecular dynamics simulations results highlighted that the multi-target-directed ligand6nstabilizes the native α-helix conformation of the Aβ42monomer and induces a sizable destabilization in the Aβ42protofibril structure.
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Affiliation(s)
- Anupamjeet Kaur
- Department of Chemistry
- Faculty of Basic and Applied Sciences
- Sri Guru Granth Sahib World University
- Fatehgarh Sahib-140406
- India
| | - Suniba Shuaib
- Department of Chemistry
- Faculty of Basic and Applied Sciences
- Sri Guru Granth Sahib World University
- Fatehgarh Sahib-140406
- India
| | - Deepti Goyal
- Department of Chemistry
- Faculty of Basic and Applied Sciences
- Sri Guru Granth Sahib World University
- Fatehgarh Sahib-140406
- India
| | - Bhupesh Goyal
- School of Chemistry & Biochemistry
- Thapar Institute of Engineering & Technology
- Patiala-147004
- India
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Zhong S, Huang K, Xiao Z, Sheng X, Li Y, Duan L. Binding Mechanism of Thrombin–Ligand Systems Investigated by a Polarized Protein-Specific Charge Force Field and Interaction Entropy Method. J Phys Chem B 2019; 123:8704-8716. [DOI: 10.1021/acs.jpcb.9b08064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Susu Zhong
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China
| | - Kaifang Huang
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China
| | - Zhengrong Xiao
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China
| | - Xiehuang Sheng
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Yuchen Li
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China
| | - Lili Duan
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China
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Kaur A, Narang SS, Kaur A, Mann S, Priyadarshi N, Goyal B, Singhal NK, Goyal D. Multifunctional Mono-Triazole Derivatives Inhibit Aβ42 Aggregation and Cu2+-Mediated Aβ42 Aggregation and Protect Against Aβ42-Induced Cytotoxicity. Chem Res Toxicol 2019; 32:1824-1839. [DOI: 10.1021/acs.chemrestox.9b00168] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Amandeep Kaur
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib 140406, Punjab, India
| | - Simranjeet Singh Narang
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib 140406, Punjab, India
| | - Anupamjeet Kaur
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib 140406, Punjab, India
| | - Sukhmani Mann
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib 140406, Punjab, India
| | - Nitesh Priyadarshi
- National Agri-Food Biotechnology Institute, S.A.S. Nagar 140306, Punjab, India
| | - Bhupesh Goyal
- School of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala 147004, Punjab, India
| | - Nitin Kumar Singhal
- National Agri-Food Biotechnology Institute, S.A.S. Nagar 140306, Punjab, India
| | - Deepti Goyal
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib 140406, Punjab, India
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