1
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Chang C, Jin X, Bai H, Zhang F, Chen L. Molecular Dynamics Simulation for the Acidic Compounds Retention Mechanism Study on Octyl-Quaternary Ammonium Mixed-Mode Stationary Phase. J Chromatogr Sci 2024; 62:962-971. [PMID: 38803160 DOI: 10.1093/chromsci/bmae036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 03/17/2024] [Indexed: 05/29/2024]
Abstract
With the widespread application of mixed-mode chromatography in separation analysis, it is becoming increasingly important to study its retention mechanism. The retention behavior of acidic compounds on mixed-mode octyl-quaternary ammonium (Sil-C8-QA) columns was investigated by computer simulation. Firstly, the benzoic acid homologues were used as the analytes, and the simulation model was constructed by the Materials Studio. Geometric optimization, annealing and molecular dynamics (MD) simulation of these complexes resulted in optimized conformations. The binding energy, mean square displacement (MSD) and torsion angle distribution generated by MD simulation were then analyzed. The results showed that the more negative binding energy, the greater the MSD and the narrower the torsion angle distribution, indicating that the stationary phase behaves with stronger interaction and retention. The retention behavior of five acidic drugs on the Sil-C8-QA column was then successfully explained by simulation. Acidic drugs are more retentive on the mixed-mode column due to the more substantial interaction brought by the reversed-phase/ion-exchange mixed-mode mechanism compared to other single-mode columns. This simulation method is expected to provide ideas for studying the separation mechanism and predicting the retention behavior of more complex samples.
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Affiliation(s)
- Chaoqun Chang
- Pharmaceutical Analysis Department, School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, 92 Weijin Road, Tianjin 300072, China
| | - Xinghua Jin
- Pharmaceutical Analysis Department, School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, 92 Weijin Road, Tianjin 300072, China
| | - Hui Bai
- Pharmaceutical Analysis Department, School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, 92 Weijin Road, Tianjin 300072, China
| | - Fan Zhang
- Pharmaceutical Analysis Department, School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, 92 Weijin Road, Tianjin 300072, China
| | - Lei Chen
- Pharmaceutical Analysis Department, School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, 92 Weijin Road, Tianjin 300072, China
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2
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Murugesan B, Subramanian A, Bakthavachalam S, Rajendran K, Raju S, Gabriel S. Molecular insights of anticancer potential of usnic acid towards cervical cancer target proteins: An in silico validation for novel anti-cancer compound from lichens. J Biomol Struct Dyn 2024; 42:9475-9493. [PMID: 37697733 DOI: 10.1080/07391102.2023.2252076] [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: 04/02/2023] [Accepted: 08/20/2023] [Indexed: 09/13/2023]
Abstract
Usnic acid is a marker compound produced from numerous lichens (symbiotic association of mycobiont and phycobiont) possessing higher bioavailability, potent and selective against cancer cells. Usnic acid is an underutilized and well-documented anti-cancer compound from lichens and its activity is not yet documented against cervical cancer. The main aim of the present research is to screen the anti-cancer potential of usnic acid against cervical cancer target proteins. The drug-likeness validation of usnic acid shows nil violations against all drug-likeness rules when compared with all three screened anti-cancer standard drugs and shows some violation in drug likeness prediction. Further, ADMET screening reveals usnic acids shows effective pharmacokinetic profiles with good bioactivity scores, essential for drug delivery and metabolism. DFT analysis of usnic acid reveals less energy gap (-0.1184), hardness (0.0592 eV), and high softness (16.8918 eV) scores against three anti-cancer drug DFT scores. Molecular docking study shows usnic acid possesses excellent binding affinity with all the nine screened cervical cancer target proteins with docking scores ranging from -6.9 to -9.1 kcal/mol. Three anti-cancer drugs showed docking scores with a range of -5.2 to -8.4 kcal/mol. Further, four top-scored complexes were taken for molecular dynamic simulation study reveal that usnic acid complexes (1KTZ-usnic acid and 2BIM-usnic acid) possess good simulation trajectories with cervical cancer target proteins than the selected anti-cancer drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Balasubramanian Murugesan
- Department of Biotechnology, Vivekanandha Arts and Science College for Women, Salem, Tamilnadu, India
| | - Anandhi Subramanian
- Department of Biotechnology, Vivekanandha Arts and Science College for Women, Salem, Tamilnadu, India
| | - Subha Bakthavachalam
- Department of Microbiology, Vivekanandha Arts and Science College for Women, Salem, Tamilnadu, India
| | - Kavitha Rajendran
- Department of Microbiology, Vivekanandha Arts and Science College for Women, Salem, Tamilnadu, India
| | - Sowndarya Raju
- Department of Biochemistry, Vivekanandha Arts and Science College for Women, Salem, Tamilnadu, India
| | - Subha Gabriel
- Department of Biochemistry, Vivekanandha Arts and Science College for Women, Salem, Tamilnadu, India
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3
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Bokatyi AN, Dubashynskaya NV, Skorik YA. Chemical modification of hyaluronic acid as a strategy for the development of advanced drug delivery systems. Carbohydr Polym 2024; 337:122145. [PMID: 38710553 DOI: 10.1016/j.carbpol.2024.122145] [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: 02/07/2024] [Revised: 03/28/2024] [Accepted: 04/08/2024] [Indexed: 05/08/2024]
Abstract
Hyaluronic acid (HA) has emerged as a promising biopolymer for various biomedical applications due to its biocompatibility, biodegradability, and intrinsic ability to interact with cell surface receptors, making it an attractive candidate for drug delivery systems and tissue engineering. Chemical modification of HA has opened up versatile possibilities to tailor its properties, enabling the development of advanced drug delivery systems and biomaterials with enhanced functionalities and targeted applications. This review analyzes the strategies and applications of chemically modified HA in the field of drug delivery and biomaterial development. The first part of the review focuses on the different methods and functional groups used for the chemical modification of HA, highlighting the impact of these modifications on its physicochemical properties, degradation behavior and interactions with drugs. The second part of the review evaluates the use of chemically modified HA in the development of advanced biomedical materials including nano- and microparticles, hydrogels and mucoadhesive materials with tailored drug release profiles, site-specific targeting and stimuli-responsive behavior. Thus, the review consolidates the current advances and future perspectives in the field of chemical modification of HA, underscoring its immense potential to drive the development of advanced drug delivery systems and biomaterials with diverse biomedical applications.
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Affiliation(s)
- Anton N Bokatyi
- Institute of Macromolecular Compounds of the Russian Academy of Sciences, Bolshoi VO 31, St. Petersburg 199004, Russian Federation
| | - Natallia V Dubashynskaya
- Institute of Macromolecular Compounds of the Russian Academy of Sciences, Bolshoi VO 31, St. Petersburg 199004, Russian Federation
| | - Yury A Skorik
- Institute of Macromolecular Compounds of the Russian Academy of Sciences, Bolshoi VO 31, St. Petersburg 199004, Russian Federation.
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4
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Mani M, Vellusamy M, Rathinavel T, Vadivel P, Dauchez M, Khan R, Aroulmoji V. In silico validation of hyaluronic acid - drug conjugates based targeted drug delivery for the treatment of COVID-19. J Biomol Struct Dyn 2024:1-15. [PMID: 38533826 DOI: 10.1080/07391102.2024.2328745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 03/05/2024] [Indexed: 03/28/2024]
Abstract
The impact of COVID-19 urges scientists to develop targeted drug delivery to manage Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) viral infections with a fast recovery rate. The aim of the study is to develop Hyaluronic Acid (HA) drug conjugates of viral drugs to target two important enzymes (Mpro and PLpro) of SARS-CoV-2. Three antiviral drugs, namely Dexamethasone (DEX), Favipiravir (FAV), and Remdesivir (REM), were chosen for HA conjugation due to their reactive functional groups. Free forms of drugs (DEX, FAV, REM) and HA drug conjugates (HA-DEX, HA-FAV, HA-REM, HA-RHA, HA-RHE) were validated against Mpro (PDB ID 6LU7) and PLpro (PDB 7LLZ), which play an essential role in the replication and reproduction of the SARS-CoV-2 virus. The results of the present study revealed that HA-drug conjugates possess higher binding affinity and the best docking score towards the Mpro and PLpro target proteins of SARS-CoV-2 than their free forms of drugs. ADMET screening resulted that HA-drug conjugates exhibited better pharmacokinetic profiles than their pure forms of drugs. Further, molecular dynamic simulation studies, essential dynamics and free energy landscape analyses show that HA antiviral drug conjugates possess good trajectories and energy status, with the PLpro target protein (PDB 7LLZ) of SARS-CoV-2 through long-distance (500 ns) simulation screening. The research work recorded the best drug candidate for Cell-Targeted Drug Delivery (CTDD) for SARS-CoV-2-infected cells through hyaluronic acid conjugates of antiviral drugs.
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Affiliation(s)
- Mohan Mani
- Centre for Research & Development, Mahendra Engineering College (Autonomous), Mallasamudram, Namakkal (Dt.), Tamil Nadu, India
| | - Mahesh Vellusamy
- Universite ́ de Reims Champagne Ardenne, CNRS, MEDyC UMR 7369, Reims, France
| | | | - Pullar Vadivel
- Department of Chemistry, Salem Sowdeswari College for Women, Salem (Dt.), Tamil Nadu, India
| | - Manuel Dauchez
- Universite ́ de Reims Champagne Ardenne, CNRS, MEDyC UMR 7369, Reims, France
| | - Riaz Khan
- Department of Chemistry, Rumsey, Sonning, Berkshire, UK
| | - Vincent Aroulmoji
- Centre for Research & Development, Mahendra Engineering College (Autonomous), Mallasamudram, Namakkal (Dt.), Tamil Nadu, India
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5
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Baby PN. Immunomodulatory and anticytokine therapeutic potential of three Indian spices constituents and its hyaluronic acid conjugates for prevention and post COVID-19 complications: a computational modeling approach. J Biomol Struct Dyn 2024:1-21. [PMID: 38444326 DOI: 10.1080/07391102.2024.2310202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/19/2024] [Indexed: 03/07/2024]
Abstract
Targeted drug delivery to SARS-CoV-2 host target proteins for preventing or blocking COVID-19 infection is making serious concern during COVID-19 pandemic and its consequent waves around the globe. People seek reliable, effective folkloric preventive medication for immediate and precautionary relief from COVID-19. These folkloric medicines were effective and saved many patients during the past COVID-19 pandemic. The current research study aims to deliver antiviral Indian spices phytocompounds and their hyaluronic acid conjugates to human host target proteins (ACE-2, TNF-α, IL-6, IL-1β, PAR-1) of SARS-CoV-2 to inhibit virus propagation and also to regulate early clinical complications of COVID-19. Targeted drug delivery of hyaluronic acid conjugated traditional natural bioactive agent produces more effective and fewer side effects in delivering novel drugs to human host proteins of COVID-19. In silico molecular docking study of six phytocompounds from three Indian spices and standard drug atazanavir and its hyaluronic acid conjugates reveals that phytocompounds and its hyaluronic acid conjugates possess high affinity to binding pockets of SARS-CoV-2 human host targets with more binding affinity scores. Most notably HA cyclocurcumin exhibit a docking score -9.9 kcal/mol against ACE-2 (PDB ID 1R42) target protein similarly HA-Hydrazinocurcumin exhibit a docking score -9.8 kcal/mol against PAR-1 (PDB ID 3VW7). ADMET validation of phytocompounds and their hyaluronic acid conjugates reveals its best pharmacokinetic profile over standard antiviral drug especially HA cyclocurcumin conjugate possesses high HIA (86%) and good pharmacokinetic profiles. DFT analysis affirms the reason behind the higher binding affinity of hyaluronic acid conjugates of spices phytocompounds towards all screened target proteins especially HA-hydrazinocurcumin conjugate possess high softness (19.1570 eV) and low hardness (0.0522 eV) values. Finally, MD simulation of best-docked compounds against ACE-2 and PAR-1 target protein revealed that hyaluronic acid conjugates of Indian spices compounds exhibit stable RMSD values and more protein-ligand interactions during simulation than hyaluronic acid conjugates of drug atazanavir.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- P Nandu Baby
- Department of Biochemistry, Amala Institute of Medical Sciences, Thrissur, Kerala, India
- Premier Healths, Edappal, Kerala, India
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6
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Kotla NG, Mohd Isa IL, Larrañaga A, Maddiboyina B, Swamy SK, Sivaraman G, Vemula PK. Hyaluronic Acid-Based Bioconjugate Systems, Scaffolds, and Their Therapeutic Potential. Adv Healthc Mater 2023; 12:e2203104. [PMID: 36972409 DOI: 10.1002/adhm.202203104] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 03/04/2023] [Indexed: 03/29/2023]
Abstract
In recent years, the development of hyaluronic acid or hyaluronan (HA) based scaffolds, medical devices, bioconjugate systems have expanded into a broad range of research and clinical applications. Research findings over the last two decades suggest that the abundance of HA in most mammalian tissues with distinctive biological roles and chemical simplicity for modifications have made it an attractive material with a rapidly growing global market. Besides its use as native forms, HA has received much interest on so-called "HA-bioconjugates" and "modified-HA systems". In this review, the importance of chemical modifications of HA, underlying rationale approaches, and various advancements of bioconjugate derivatives with their potential physicochemical, and pharmacological advantages are summarized. This review also highlights the current and emerging HA-based conjugates of small molecules, macromolecules, crosslinked systems, and surface coating strategies with their biological implications, including their potentials and key challenges discussed in detail.
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Affiliation(s)
- Niranjan G Kotla
- Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, Karnataka, 560065, India
| | - Isma Liza Mohd Isa
- Department of Anatomy, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, 56000, Malaysia
| | - Aitor Larrañaga
- Department of Mining-Metallurgy Engineering and Materials Science, POLYMAT, Faculty of Engineering, University of the Basque Country (UPV/EHU), Bilbao, 48013, Spain
| | - Balaji Maddiboyina
- Department of Medical Writing, Freyr Solutions, Hyderabad, Telangana, 500081, India
| | - Samantha K Swamy
- Thrombosis Research Center (TREC), Department of Clinical Medicine, UiT-The Arctic University of Norway, Tromsø, 9037, Norway
| | - Gandhi Sivaraman
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram, Tamil Nadu, 624302, India
| | - Praveen K Vemula
- Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, Karnataka, 560065, India
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7
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Zheng X, Wang B, Tang X, Mao B, Zhang Q, Zhang T, Zhao J, Cui S, Chen W. Absorption, metabolism, and functions of hyaluronic acid and its therapeutic prospects in combination with microorganisms: A review. Carbohydr Polym 2023; 299:120153. [PMID: 36876779 DOI: 10.1016/j.carbpol.2022.120153] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 09/21/2022] [Accepted: 09/21/2022] [Indexed: 11/25/2022]
Abstract
Hyaluronic acid (HA) is key to the stability of the internal environment of tissues. HA content in tissues gradually decreases with age, causing age-related health problems. Exogenous HA supplements are used to prevent or treat these problems including skin dryness and wrinkles, intestinal imbalance, xerophthalmia, and arthritis after absorption. Moreover, some probiotics are able to promote endogenous HA synthesis and alleviate symptoms caused by HA loss, thus introducing potential preventative or therapeutic applications of HA and probiotics. Here, we review the oral absorption, metabolism, and biological function of HA as well as the potential role of probiotics and HA in increasing the efficacy of HA supplements.
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Affiliation(s)
- Xueli Zheng
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Botao Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Bloomage Biotechnology Co., Ltd, Jinan 250000, China
| | - Xin Tang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Bingyong Mao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Qiuxiang Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Tianmeng Zhang
- Bloomage Biotechnology Co., Ltd, Jinan 250000, China; School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Shumao Cui
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
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8
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Santos ACF, Martel F, Freire CSR, Ferreira BJML. Polymeric Materials as Indispensable Tools to Fight RNA Viruses: SARS-CoV-2 and Influenza A. Bioengineering (Basel) 2022; 9:816. [PMID: 36551022 PMCID: PMC9816944 DOI: 10.3390/bioengineering9120816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/03/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Towards the end of 2019 in Wuhan, suspicions of a new dangerous virus circulating in the air began to arise. It was the start of the world pandemic coronavirus disease 2019 (COVID-19). Since then, considerable research data and review papers about this virus have been published. Hundreds of researchers have shared their work in order to achieve a better comprehension of this disease, all with the common goal of overcoming this pandemic. The coronavirus is structurally similar to influenza A. Both are RNA viruses and normally associated with comparable infection symptoms. In this review, different case studies targeting polymeric materials were appraised to highlight them as an indispensable tool to fight these RNA viruses. In particular, the main focus was how polymeric materials, and their versatile features could be applied in different stages of viral disease, i.e., in protection, detection and treatment.
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Affiliation(s)
- Ariana C. F. Santos
- CICECO-Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Fátima Martel
- Biochemistry Unit, Biomedicine Department, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
- I3S-Institute of Research and Innovation in Health, University of Porto, 4200-135 Porto, Portugal
| | - Carmen S. R. Freire
- CICECO-Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Bárbara J. M. L. Ferreira
- CICECO-Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
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9
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Buckley C, Murphy EJ, Montgomery TR, Major I. Hyaluronic Acid: A Review of the Drug Delivery Capabilities of This Naturally Occurring Polysaccharide. Polymers (Basel) 2022; 14:polym14173442. [PMID: 36080515 PMCID: PMC9460006 DOI: 10.3390/polym14173442] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
The inclusion of physiologically active molecules into a naturally occurring polymer matrix can improve the degradation, absorption, and release profile of the drug, thus boosting the therapeutic impact and potentially even reducing the frequency of administration. The human body produces significant amounts of polysaccharide hyaluronic acid, which boasts exceptional biocompatibility, biodegradability, and one-of-a-kind physicochemical features. In this review, we will examine the clinical trials currently utilizing hyaluronic acid and address the bright future of this versatile polymer, as well as summarize the numerous applications of hyaluronic acid in drug delivery and immunomodulation.
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Affiliation(s)
- Ciara Buckley
- PRISM Research Institute, Technological University of the Shannon, N37 HD68 Athlone, Ireland
- Biosciences Research Institute, Technological University of the Shannon, V94 EC5T Limerick, Ireland
| | - Emma J. Murphy
- PRISM Research Institute, Technological University of the Shannon, N37 HD68 Athlone, Ireland
- LIFE Research Institute, Technological University of the Shannon, V94 EC5T Limerick, Ireland
| | - Therese R. Montgomery
- School of Science and Computing, Atlantic Technological University, H91 T8NW Galway, Ireland
| | - Ian Major
- PRISM Research Institute, Technological University of the Shannon, N37 HD68 Athlone, Ireland
- Correspondence:
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Selvaraj V, Rathinavel T, Ammashi S, Nasir Iqbal M. Polyphenolic Phytochemicals Exhibit Promising SARS-COV-2 Papain Like Protease (PLpro) Inhibition Validated through a Computational Approach. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2103578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Vasuki Selvaraj
- Department of Biotechnology, Sona College of Arts and Science, Salem, India
| | | | - Subramanian Ammashi
- PG and Research Department of Biochemistry, Rajah Serfoji Government College, Thanjavur, India
| | - Muhammad Nasir Iqbal
- Department of Bioinformatics, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
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11
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Gao K, Wang R, Chen J, Cheng L, Frishcosy J, Huzumi Y, Qiu Y, Schluckbier T, Wei X, Wei GW. Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2. Chem Rev 2022; 122:11287-11368. [PMID: 35594413 PMCID: PMC9159519 DOI: 10.1021/acs.chemrev.1c00965] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite tremendous efforts in the past two years, our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus-host interactions, immune response, virulence, transmission, and evolution is still very limited. This limitation calls for further in-depth investigation. Computational studies have become an indispensable component in combating coronavirus disease 2019 (COVID-19) due to their low cost, their efficiency, and the fact that they are free from safety and ethical constraints. Additionally, the mechanism that governs the global evolution and transmission of SARS-CoV-2 cannot be revealed from individual experiments and was discovered by integrating genotyping of massive viral sequences, biophysical modeling of protein-protein interactions, deep mutational data, deep learning, and advanced mathematics. There exists a tsunami of literature on the molecular modeling, simulations, and predictions of SARS-CoV-2 and related developments of drugs, vaccines, antibodies, and diagnostics. To provide readers with a quick update about this literature, we present a comprehensive and systematic methodology-centered review. Aspects such as molecular biophysics, bioinformatics, cheminformatics, machine learning, and mathematics are discussed. This review will be beneficial to researchers who are looking for ways to contribute to SARS-CoV-2 studies and those who are interested in the status of the field.
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Affiliation(s)
- Kaifu Gao
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Rui Wang
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jiahui Chen
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Limei Cheng
- Clinical
Pharmacology and Pharmacometrics, Bristol
Myers Squibb, Princeton, New Jersey 08536, United States
| | - Jaclyn Frishcosy
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuta Huzumi
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuchi Qiu
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Tom Schluckbier
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Xiaoqi Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Guo-Wei Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
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12
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Thirumalaisamy R, Aroulmoji V, Iqbal MN, Saride S, Bhuvaneswari M, Deepa M, Sivasankar C, Khan R. Molecular insights of hyaluronic acid - ethambutol and hyaluronic acid - isoniazid drug conjugates act as promising novel drugs for the treatment of tuberculosis. J Biomol Struct Dyn 2022; 41:3562-3573. [PMID: 35293842 DOI: 10.1080/07391102.2022.2051748] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The present study examines cellular targeted drug delivery (CTDD) pattern of two novel Hyaluronic acid (HA) Tuberculosis Drug (TB) conjugates and its efficacy and strong binding affinity towards TB molecular protein targets. Two TB drugs ethambutol (EB) and isoniazid (IN) and their Hyaluronic acid conjugates (HA-EB & HA-IN) were tested for its metabolism, toxicity and excretion prediction through In silico tools they revealed hyaluronic acid conjugate of two TB drugs exhibited good drug profile over their free form of TB drugs. Further these four molecules subjected to In silico molecular docking study with four potential Mycobacterium tuberculosis target proteins (3PD8, 4Y0L, 5DZK and 6GAU). Molecular docking study revealed that hyaluronic conjugates (HA-EB & HA-IN) exhibit significant binding affinity and excellent docking scores with all screened molecular protein targets of TB over their free form of drug. Further molecular dynamic simulation was calculated for the four drug molecules (EB, IN, HA- EB & HA-IN) with DNA gyrase enzyme (PDB ID 6GAU) of Mycobacterium tuberculosis and the MDS results revealed that both the conjugates with the TB target protein possessed good number of interaction with binding pocket residues and good simulation scores than the free form of drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- R Thirumalaisamy
- Department of Biotechnology, Sona College of Arts and Science, Salem, Tamil Nadu, India
| | - V Aroulmoji
- Centre for Research & Development, Mahendra Engineering College (Autonomous), Mallasamudram, Namakkal, Tamil Nadu, India
| | | | - Shreyas Saride
- School of Behavioral and Brain Sciences, The University of Texas at Dallas, Richardson, TX, United States
| | - M Bhuvaneswari
- Department of Biotechnology, Sona College of Arts and Science, Salem, Tamil Nadu, India
| | - M Deepa
- Postgraduate and Research Department of Chemistry, Muthurangam Govt. Arts College, Vellore, India
| | - C Sivasankar
- Catalysis and Energy Laboratory, Department of Chemistry, Pondicherry University, Kalapet, Pondicherry, India
| | - Riaz Khan
- Rumsey, Berkshire, England, United Kingdom
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Velu P, Rathinavel T, Kumarasamy S, Iqbal MN, Noor H, Ikram A, Rajamanickam K, Shanmugam G. Whole genome analysis and homology modeling of SARS-CoV-2 Indian isolate reveals potent FDA approved drug choice for treating COVID-19. J Biomol Struct Dyn 2022; 41:2772-2788. [PMID: 35139758 DOI: 10.1080/07391102.2022.2038272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Coronaviruses have caused enough devastation in the last two decades. These viruses have some rare features while sharing some common features. Novel coronavirus disease (nCoV-19) caused an outbreak with a fatality rate of 5%. It emerged from China and spread into many countries. The present research focused on genome analysis of Indian nCoV-19 Isolate and its translational product subjected to homology modeling and its subsequent molecular simulations to find out potent FDA approved drug for treating COVID-19. Phylogenetic analysis of SARS-CoV-2 Indian isolate shows close resemblance with 17 countries SARS-CoV-2 isolates. Homology modeling of four non-structural proteins translational product of Indian SARS-CoV-2 genome shows high similarity and allowed regions with the existing PDB deposited SARS-CoV-2 target proteins. Finally, these four generated proteins show more affinity with cobicistat, remdesivir and indinavir out of 14 screened FDA approved drugs in molecular docking which is further proven by molecular dynamics simulation and MMGBSA analysis of target ligand complex with best simulation trajectories. Overall our present research findings is that three proposed drugs namely cobicistat, remdesivir and indinavir showed higher interaction with the model SARS-CoV-2 viral target proteins from the Indian nCoV-19 isolate. These compounds could be used as a starting point for the creation of active antiviral drugs to combat the deadly COVID-19 virus during global pandemic and its subsequent viral infection waves across the globe.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Periyannan Velu
- Department of Biotechnology and Biochemistry, Annamalai University, Chidambaram, Tamil Nadu, India
| | | | - Suresh Kumarasamy
- PG and Research Centre in Biotechnology, MGR College, Adhiyamaan Educational Research Institute, Hosur, Tamil Nadu, India
| | - Muhammad Nasir Iqbal
- Department of Biosciences, COMSATS University, Islamabad Campus, Islamabad, Pakistan
| | - Hasnat Noor
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Ayesha Ikram
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Karthika Rajamanickam
- Department of Biotechnology, Vivekanandha College of Arts and Sciences for Women (Autonomous), Namakkal, Tamil Nadu, India
| | - Gnanendra Shanmugam
- Department of Biotechnology, Mahendra Arts and Science College, Namakkal, Tamil Nadu, India
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Shariatinia Z, Pourzadi N. Designing novel anticancer drug release vehicles based on mesoporous functionalized MCM-41 nanoparticles. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130754] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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