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Bhatia S, Singh M, Sharma P, Mujwar S, Singh V, Mishra KK, Singh TG, Singh T, Ahmad SF. Scaffold Morphing and In Silico Design of Potential BACE-1 (β-Secretase) Inhibitors: A Hope for a Newer Dawn in Anti-Alzheimer Therapeutics. Molecules 2023; 28:6032. [PMID: 37630283 PMCID: PMC10459662 DOI: 10.3390/molecules28166032] [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: 07/24/2023] [Revised: 08/04/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Alzheimer's disease (AD) is the prime cause of 65-80% of dementia cases and is caused by plaque and tangle deposition in the brain neurons leading to brain cell degeneration. β-secretase (BACE-1) is a key enzyme responsible for depositing extracellular plaques made of β-amyloid protein. Therefore, efforts are being applied to develop novel BACE-1 enzyme inhibitors to halt plaque build-up. In our study, we analyzed some Elenbecestat analogues (a BACE-1 inhibitor currently in clinical trials) using a structure-based drug design and scaffold morphing approach to achieve a superior therapeutic profile, followed by in silico studies, including molecular docking and pharmacokinetics methodologies. Among all the designed compounds, SB306 and SB12 showed good interactions with the catalytic dyad motifs (Asp228 and Asp32) of the BACE-1 enzyme with drug-likeliness properties and a high degree of thermodynamic stability confirmed by the molecular dynamic and stability of the simulated system indicating the inhibitory nature of the SB306 and SB12 on BACE 1.
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Affiliation(s)
- Shiveena Bhatia
- Chitkara College of Pharmacy, Chitkara University, Rajpura 140401, Punjab, India (P.S.); (S.M.); (T.G.S.)
| | - Manjinder Singh
- Chitkara College of Pharmacy, Chitkara University, Rajpura 140401, Punjab, India (P.S.); (S.M.); (T.G.S.)
| | - Pratibha Sharma
- Chitkara College of Pharmacy, Chitkara University, Rajpura 140401, Punjab, India (P.S.); (S.M.); (T.G.S.)
| | - Somdutt Mujwar
- Chitkara College of Pharmacy, Chitkara University, Rajpura 140401, Punjab, India (P.S.); (S.M.); (T.G.S.)
| | - Varinder Singh
- Department of Pharmaceutical Sciences and Technology, Maharaja Ranjit Singh Punjab Technical University, Bathinda 151001, Punjab, India;
| | - Krishna Kumar Mishra
- Chitkara University Institute of Engineering and Technology, Chitkara University, Rajpura 140401, Punjab, India;
| | - Thakur Gurjeet Singh
- Chitkara College of Pharmacy, Chitkara University, Rajpura 140401, Punjab, India (P.S.); (S.M.); (T.G.S.)
| | - Tanveer Singh
- Department of Neuroscience and Experimental Therapeutics, College of Medicine, Texas A&M Health Science Center, College Station, TX 77807, USA
| | - Sheikh Fayaz Ahmad
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
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Daoui O, Elkhattabi S, Bakhouch M, Belaidi S, Bhandare RR, Shaik AB, Mali SN, Chtita S. Cyclohexane-1,3-dione Derivatives as Future Therapeutic Agents for NSCLC: QSAR Modeling, In Silico ADME-Tox Properties, and Structure-Based Drug Designing Approach. ACS OMEGA 2023; 8:4294-4319. [PMID: 36743017 PMCID: PMC9893467 DOI: 10.1021/acsomega.2c07585] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 12/29/2022] [Indexed: 05/20/2023]
Abstract
The abnormal expression of the c-Met tyrosine kinase has been linked to the proliferation of several human cancer cell lines, including non-small-cell lung cancer (NSCLC). In this context, the identification of new c-Met inhibitors based on heterocyclic small molecules could pave the way for the development of a new cancer therapeutic pathway. Using multiple linear regression (MLR)-quantitative structure-activity relationship (QSAR) and artificial neural network (ANN)-QSAR modeling techniques, we look at the quantitative relationship between the biological inhibitory activity of 40 small molecules derived from cyclohexane-1,3-dione and their topological, physicochemical, and electronic properties against NSCLC cells. In this regard, screening methods based on QSAR modeling with density-functional theory (DFT) computations, in silico pharmacokinetic/pharmacodynamic (ADME-Tox) modeling, and molecular docking with molecular electrostatic potential (MEP) and molecular mechanics-generalized Born surface area (MM-GBSA) computations were used. Using physicochemical (stretch-bend, hydrogen bond acceptor, Connolly molecular area, polar surface area, total connectivity) and electronic (total energy, highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy levels) molecular descriptors, compound 6d is identified as the optimal scaffold for drug design based on in silico screening tests. The computer-aided modeling developed in this study allowed us to design, optimize, and screen a new class of 36 small molecules based on cyclohexane-1,3-dione as potential c-Met inhibitors against NSCLC cell growth. The in silico rational drug design approach used in this study led to the identification of nine lead compounds for NSCLC therapy via c-Met protein targeting. Finally, the findings are validated using a 100 ns series of molecular dynamics simulations in an aqueous environment on c-Met free and complexed with samples of the proposed lead compounds and Foretinib drug.
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Affiliation(s)
- Ossama Daoui
- Laboratory
of Engineering, Systems and Applications, National School of Applied
Sciences, Sidi Mohamed Ben Abdellah-Fez
University, BP Box 72, Fez30000, Morocco
| | - Souad Elkhattabi
- Laboratory
of Engineering, Systems and Applications, National School of Applied
Sciences, Sidi Mohamed Ben Abdellah-Fez
University, BP Box 72, Fez30000, Morocco
| | - Mohamed Bakhouch
- Laboratory
of Bioorganic Chemistry, Department of Chemistry, Faculty of Sciences, Chouaïb Doukkali University, P.O. Box 24, 24000El Jadida, Morocco
| | - Salah Belaidi
- Group
of Computational and Medicinal Chemistry, LMCE Laboratory, University of Biskra,
BP 145, Biskra707000, Algeria
| | - Richie R. Bhandare
- Department
of Pharmaceutical Sciences, College of Pharmacy & Health Sciences, Ajman University, Ajman346, United Arab Emirates
- Center of Medical and Bio-allied
Health Sciences Research, Ajman University, Ajman P.O. Box 340, 346, United Arab Emirates
| | - Afzal B. Shaik
- St. Mary’s
College of Pharmacy, St. Mary’s Group
of Institutions Guntur, Affiliated to Jawaharlal Nehru Technological
University Kakinada, Chebrolu, Guntur, Andhra Pradesh522212, India
| | - Suraj N. Mali
- Department
of Pharmacy, Government College of Pharmacy, Karad, Affiliated to Shivaji University, Kolhapur, Maharashtra415124, India
| | - Samir Chtita
- Laboratory
of Analytical and Molecular Chemistry, Faculty of Sciences Ben M’Sik, Hassan II University of Casablanca, Casablanca7955, Morocco
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Synthesis, biological evaluation and molecular docking study of benzimidazole derivatives as α-glucosidase inhibitors and anti-diabetes candidates. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Feng Q, Yang W, Peng Z, Wang G. Recent advances in the synthetic thymidine phosphorylase inhibitors for cancer therapy. Eur J Pharmacol 2022; 934:175319. [DOI: 10.1016/j.ejphar.2022.175319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/16/2022] [Accepted: 10/04/2022] [Indexed: 11/03/2022]
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Yakan H, Çakmak Ş, Buruk O, Veyisoğlu A, Muğlu H, Türköz Karakullukçu N. New 5-methylisatin including thiocarbohydrazones: preparation, structure elucidation and antimicrobial activity. RESEARCH ON CHEMICAL INTERMEDIATES 2022. [DOI: 10.1007/s11164-022-04799-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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