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Tee WV, Berezovsky IN. Allosteric drugs: New principles and design approaches. Curr Opin Struct Biol 2024; 84:102758. [PMID: 38171188 DOI: 10.1016/j.sbi.2023.102758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024]
Abstract
Focusing on an important biomedical implication of allostery - design of allosteric drugs, we describe characteristics of allosteric sites, effectors, and their modes of actions distinguishing them from the orthosteric counterparts and calling for new principles and protocols in the quests for allosteric drugs. We show the importance of considering both binding affinity and allosteric signaling in establishing the structure-activity relationships (SARs) toward design of allosteric effectors, arguing that pairs of allosteric sites and their effector ligands - the site-effector pairs - should be generated and adjusted simultaneously in the framework of what we call directed design protocol. Key ideas and approaches for designing allosteric effectors including reverse perturbation, targeted and agnostic analysis are also discussed here. Several promising computational approaches are highlighted, along with the need for and potential advantages of utilizing generative models to facilitate discovery/design of new allosteric drugs.
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Affiliation(s)
- Wei-Ven Tee
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A∗STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671.
| | - Igor N Berezovsky
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A∗STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671; Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, 117579, Singapore.
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Tiwari G, Chauhan MS, Sharma D. In silico study of inhibition activity of boceprevir drug against 2019-nCoV main protease. Z NATURFORSCH C 2024; 79:1-12. [PMID: 38156366 DOI: 10.1515/znc-2023-0117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 12/11/2023] [Indexed: 12/30/2023]
Abstract
Boceprevir drug is a ketoamide serine protease inhibitor with a linear peptidomimetic structure that exhibits inhibition activity against 2019-nCoV main protease. This paper reports electronic properties of boceprevir and its molecular docking as well as molecular dynamics simulation analysis with protein receptor. For this, the equilibrium structure of boceprevir has been obtained by DFT at B3LYP and ωB97XD levels with 6-311+G(d,p) basis set in gas and water mediums. HOMO-LUMO and absorption spectrum analysis have been used to evaluate the boceprevir's toxicity and photosensitivity, respectively. Molecular docking simulation has been performed to test the binding affinity of boceprevir with 2019-nCoV MPRO; which rendered a variety of desirable binding locations between the ligand and target protein's residue positions. The optimum binding location has been considered for molecular dynamics simulation. The findings have been addressed to clarify the boceprevir drug efficacy against the 2019-nCoV MPRO.
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Affiliation(s)
- Gargi Tiwari
- Department of Physics, Patna University, Patna-800005, India
| | | | - Dipendra Sharma
- Department of Physics, DDU Gorakhpur University, Gorakhpur-273009, India
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Raza SHA, Zhong R, Yu X, Zhao G, Wei X, Lei H. Advances of Predicting Allosteric Mechanisms Through Protein Contact in New Technologies and Their Application. Mol Biotechnol 2023:10.1007/s12033-023-00951-4. [PMID: 37957479 DOI: 10.1007/s12033-023-00951-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/12/2023] [Indexed: 11/15/2023]
Abstract
Allostery is an intriguing phenomenon wherein the binding activity of a biological macromolecule is modulated via non-canonical binding site, resulting in synchronized functional changes. The mechanics underlying allostery are relatively complex and this review is focused on common methodologies used to study allostery, such as X-ray crystallography, NMR spectroscopy, and HDXMS. Different methodological approaches are used to generate data in different scenarios. For example, X-ray crystallography provides high-resolution structural information, NMR spectroscopy offers dynamic insights into allosteric interactions in solution, and HDXMS provides information on protein dynamics. The residue transition state (RTS) approach has emerged as a critical tool in understanding the energetics and conformational changes associated with allosteric regulation. Allostery has significant implications in drug discovery, gene transcription, disease diagnosis, and enzyme catalysis. Enzymes' catalytic activity can be modulated by allosteric regulation, offering opportunities to develop novel therapeutic alternatives. Understanding allosteric mechanisms associated with infectious organisms like SARS-CoV and bacterial pathogens can aid in the development of new antiviral drugs and antibiotics. Allosteric mechanisms are crucial in the regulation of a variety of signal transduction and cell metabolism pathways, which in turn govern various cellular processes. Despite progress, challenges remain in identifying allosteric sites and characterizing their contribution to a variety of biological processes. Increased understanding of these mechanisms can help develop allosteric systems specifically designed to modulate key biological mechanisms, providing novel opportunities for the development of targeted therapeutics. Therefore, the current review aims to summarize common methodologies that are used to further our understanding of allosteric mechanisms. In conclusion, this review provides insights into the methodologies used for the study of allostery, its applications in in silico modeling, the mechanisms underlying antibody allostery, and the ongoing challenges and prospects in advancing our comprehension of this intriguing phenomenon.
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Affiliation(s)
- Sayed Haidar Abbas Raza
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Nation-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan, 512005, China
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Ruimin Zhong
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan, 512005, China
| | - Xiaoting Yu
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Nation-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou, 510642, China
| | - Gang Zhao
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Nation-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou, 510642, China
| | - Xiaoqun Wei
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Nation-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou, 510642, China
| | - Hongtao Lei
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Nation-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
- Licheng Detection and Certification Group Co., Ltd., Zhongshan, 528403, Guangdong, China.
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Panigrahi R, Kailasam S. Mapping allosteric pathway in NIa-Pro using computational approach. QUANTITATIVE BIOLOGY 2023. [DOI: 10.15302/j-qb-022-0296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Green and efficient one-pot three-component synthesis of novel drug-like furo[2,3–d]pyrimidines as potential active site inhibitors and putative allosteric hotspots modulators of both SARS-CoV-2 MPro and PLPro. Bioorg Chem 2023; 135:106390. [PMID: 37037129 PMCID: PMC9883075 DOI: 10.1016/j.bioorg.2023.106390] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/17/2023] [Accepted: 01/20/2023] [Indexed: 01/29/2023]
Abstract
In this paper, an environmentally benign, convenient, and efficient one-pot three-component reaction has been developed for the regioselective synthesis of novel 5-aroyl(or heteroaroyl)-6-(alkylamino)-1,3-dimethylfuro[2,3-d]pyrimidine-2,4(1H,3H)-diones (4a‒n) through the sequential condensation of aryl(or heteroaryl)glyoxal monohydrates (1a‒g), 1,3-dimethylbarbituric acid (2), and alkyl(viz. cyclohexyl or tert-butyl)isocyanides (3a or 3b) catalyzed by ultra-low loading ZrOCl2•8H2O (just 2 mol%) in water at 50 ˚C. After synthesis and characterization of the mentioned furo[2,3-d]pyrimidines (4a‒n), their multi-targeting inhibitory properties were investigated against the active site and putative allosteric hotspots of both SARS-CoV-2 main protease (MPro) and papain-like protease (PLPro) based on molecular docking studies and compare the attained results with various medicinal compounds which approximately in three past years were used, introduced, and or repurposed to fight against COVID-19. Furthermore, drug-likeness properties of the mentioned small heterocyclic frameworks (4a‒n) have been explored using in silico ADMET analyses. Interestingly, the molecular docking studies and ADMET-related data revealed that the novel series of furo[2,3-d]pyrimidines (4a‒n), especially 5-(3,4-methylendioxybenzoyl)-6-(cyclohexylamino)-1,3-dimethylfuro[2,3-d]pyrimidine-2,4(1H,3H)-dione (4g) as hit one is potential COVID-19 drug candidate, can subject to further in vitro and in vivo studies. It is worthwhile to note that the protein-ligand-type molecular docking studies on the human body temperature-dependent MPro protein that surprisingly contains zincII (ZnII) ion between His41/Cys145 catalytic dyad in the active site, which undoubtedly can make new plans for designing novel SARS-CoV-2 MPro inhibitors, is performed for the first time in this paper, to the best of our knowledge.
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Cao JF, Gong Y, Wu M, Xiong L, Chen S, Huang H, Zhou X, Peng YC, Shen XF, Qu J, Wang YL, Zhang X. Molecular docking and molecular dynamics study Lianhua Qingwen granules (LHQW) treats COVID-19 by inhibiting inflammatory response and regulating cell survival. Front Cell Infect Microbiol 2022; 12:1044770. [PMID: 36506032 PMCID: PMC9729774 DOI: 10.3389/fcimb.2022.1044770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 11/08/2022] [Indexed: 11/25/2022] Open
Abstract
Purpose 2019 Coronavirus disease (COVID-19) is endangering health of populations worldwide. Latest research has proved that Lianhua Qingwen granules (LHQW) can reduce tissue damage caused by inflammatory reactions and relieve patients' clinical symptoms. However, the mechanism of LHQW treats COVID-19 is currently lacking. Therefore, we employed computer simulations to investigate the mechanism of LHQW treats COVID-19 by modulating inflammatory response. Methods We employed bioinformatics to screen active ingredients in LHQW and intersection gene targets. PPI, GO and KEGG was used to analyze relationship of intersection gene targets. Molecular dynamics simulations validated the binding stability of active ingredients and target proteins. Binding free energy, radius of gyration and the solvent accessible surface area were analyzed by supercomputer platform. Results COVID-19 had 4628 gene targets, LHQW had 1409 gene targets, intersection gene targets were 415. Bioinformatics analysis showed that intersection targets were closely related to inflammation and immunomodulatory. Molecular docking suggested that active ingredients (including: licopyranocoumarin, Glycyrol and 3-3-Oxopropanoic acid) in LHQW played a role in treating COVID-19 by acting on CSF2, CXCL8, CCR5, NLRP3, IFNG and TNF. Molecular dynamics was used to prove the binding stability of active ingredients and protein targets. Conclusion The mechanism of active ingredients in LHQW treats COVID-19 was investigated by computer simulations. We found that active ingredients in LHQW not only reduce cell damage and tissue destruction by inhibiting the inflammatory response through CSF2, CXCL8, CCR5 and IFNG, but also regulate cell survival and growth through NLRP3 and TNF thereby reducing apoptosis.
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Affiliation(s)
- Jun-Feng Cao
- Chengdu Medical College, Chengdu, China,Chengdu Medical College of Basic Medical Sciences, Chengdu, China
| | | | - Mei Wu
- Chengdu Medical College, Chengdu, China
| | - Li Xiong
- Chengdu Medical College, Chengdu, China
| | | | | | | | - Ying-chun Peng
- Chengdu Medical College, Chengdu, China,The First Affifiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Xue-fang Shen
- Chengdu Medical College, Chengdu, China,The First Affifiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Jinyu Qu
- Chengdu Medical College, Chengdu, China,The First Affifiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Yi-li Wang
- Chengdu Medical College, Chengdu, China,The First Affifiliated Hospital of Chengdu Medical College, Chengdu, China,*Correspondence: Yi-li Wang, ; Xiao Zhang,
| | - Xiao Zhang
- Chengdu Medical College, Chengdu, China,Chengdu Medical College of Basic Medical Sciences, Chengdu, China,*Correspondence: Yi-li Wang, ; Xiao Zhang,
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Berezovsky IN, Nussinov R. Multiscale Allostery: Basic Mechanisms and Versatility in Diagnostics and Drug Design. J Mol Biol 2022; 434:167751. [PMID: 35863488 DOI: 10.1016/j.jmb.2022.167751] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Igor N Berezovsky
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671, Singapore; Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, 117579, Singapore.
| | - Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboraory, National Cancer Institute, Frederick, MD 21702, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
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