1
|
Singh S, Choudhary M. Unusual Ni⋯Ni interaction in Ni(ii) complexes as potential inhibitors for the development of new anti-SARS-CoV-2 Omicron drugs. RSC Med Chem 2024; 15:895-915. [PMID: 38516589 PMCID: PMC10953495 DOI: 10.1039/d3md00601h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 01/05/2024] [Indexed: 03/23/2024] Open
Abstract
Two nickel(ii) coordination complexes [Ni(L)]2(1) and [Ni(L)]n(2) of a tetradentate Schiff base ligand (H2L) derived from 2-hydroxy-1-naphthaldehyde with ethylenediamine were synthesized, designed, and characterized via spectroscopic and single crystal XRD analyses. Both nickel(ii) complexes exhibited unusual Ni⋯Ni interactions and were fully characterized via single-crystal X-ray crystallography. Nickel(ii) complexes [Ni(L)]2(1) and [Ni(L)]n(2) crystallize in monoclinic and triclinic crystal systems with P21/c and P1̄ space groups, respectively, and revealed square planar geometry around each Ni(ii) ion. The structure of both the complexes have established the existence of a new kind of metal system containing nickel(ii)-nickel(ii) interactions with a square planar-like geometry about the nickel(ii) atoms. Both square planar Ni(ii) complexes were often stacked with relatively short Ni⋯Ni distances. The non-bonded Ni-Ni distance (Ni⋯Ni separation) seems to be 3.356 Å and 3.214 Å from the nickel atoms of [Ni(L)]2(1) and [Ni(L)]n(2), respectively. These distances are shorter than the sum of their van der Waals radii (4.80 Å) but longer than the sum of their covalent radii (2.50 Å), indicating that there is a Ni⋯Ni interaction but not a Ni-Ni bond. The discrete molecules are π-stacked and connected via weak intermolecular interactions (C-H⋯O and C-H⋯N). Cyclic voltammetry measurements were obtained for both the complexes, and their pharmacokinetic and chemoinformatics properties were also explored. Detailed structural analysis and non-covalent supramolecular interactions were investigated using single-crystal structure analysis and computational approaches. Both the unique structures show good inhibition performance for the Omicron spike proteins of the SARS CoV-2 virus. To gain insights into potential SARS-CoV-2 Omicron drugs and find inhibitors against the Omicron variants of SARS-CoV-2, we examined the molecular docking of the nickel(ii) complexes [Ni(L)]2(1) and [Ni(L)]n(2) with the SARS-CoV-2 Omicron spike protein (PDB ID: 7WK2 and 7WVO). A strong binding was predicted between Ni(ii) coordination complexes [Ni(L)]2(1) and [Ni(L)]n(2) with the SARS-CoV-2 Omicron variant receptor protein through the negative value of binding affinity. Molecular docking of Nil(ii) complexes [Ni(L)]2(1) and [Ni(L)]n(2) with a DNA duplex (PDB ID: 7D3T) and RNA (PDB ID: 7TDC) binding protein was also studied. Overall, this study suggests that Ni(ii) complexes can be considered as drug candidates against the Omicron variants of SARS-CoV-2.
Collapse
Affiliation(s)
- Simranjeet Singh
- Department of Chemistry, National Institute of Technology Patna Patna-800005 Bihar India
| | - Mukesh Choudhary
- Department of Chemistry, National Institute of Technology Patna Patna-800005 Bihar India
| |
Collapse
|
2
|
Hristova SH, Zhivkov AM. Omicron Coronavirus: pH-Dependent Electrostatic Potential and Energy of Association of Spike Protein to ACE2 Receptor. Viruses 2023; 15:1752. [PMID: 37632094 PMCID: PMC10460073 DOI: 10.3390/v15081752] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/12/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
The association of the S-protein of the SARS-CoV-2 beta coronavirus to ACE2 receptors of the human epithelial cells determines its contagiousness and pathogenicity. We computed the pH-dependent electric potential on the surface of the interacting globular proteins and pH-dependent Gibbs free energy at the association of the wild-type strain and the omicron variant. The calculated isoelectric points of the ACE2 receptor (pI 5.4) and the S-protein in trimeric form (pI 7.3, wild type), (pI 7.8, omicron variant), experimentally verified by isoelectric focusing, show that at pH 6-7, the S1-ACE2 association is conditioned by electrostatic attraction of the oppositely charged receptor and viral protein. The comparison of the local electrostatic potentials of the omicron variant and the wild-type strain shows that the point mutations alter the electrostatic potential in a relatively small area on the surface of the receptor-binding domain (RBD) of the S1 subunit. The appearance of seven charge-changing point mutations in RBD (equivalent to three additional positive charges) leads to a stronger S1-ACE2 association at pH 5.5 (typical for the respiratory tract) and a weaker one at pH 7.4 (characteristic of the blood plasma); this reveals the reason for the higher contagiousness but lower pathogenicity of the omicron variant in comparison to the wild-type strain.
Collapse
Affiliation(s)
- Svetlana H. Hristova
- Department of Medical Physics and Biophysics, Medical Faculty, Medical University—Sofia, Zdrave Str. 2, 1431 Sofia, Bulgaria;
| | - Alexandar M. Zhivkov
- Institute of Physical Chemistry, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., bl. 11, 1113 Sofia, Bulgaria
| |
Collapse
|
3
|
Giron CC, Laaksonen A, Barroso da Silva FL. Differences between Omicron SARS-CoV-2 RBD and other variants in their ability to interact with cell receptors and monoclonal antibodies. J Biomol Struct Dyn 2023; 41:5707-5727. [PMID: 35815535 DOI: 10.1080/07391102.2022.2095305] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 06/23/2022] [Indexed: 12/23/2022]
Abstract
SARS-CoV-2 remains a health threat with the continuous emergence of new variants. This work aims to expand the knowledge about the SARS-CoV-2 receptor-binding domain (RBD) interactions with cell receptors and monoclonal antibodies (mAbs). By using constant-pH Monte Carlo simulations, the free energy of interactions between the RBD from different variants and several partners (Angiotensin-Converting Enzyme-2 (ACE2) polymorphisms and various mAbs) were predicted. Computed RBD-ACE2-binding affinities were higher for two ACE2 polymorphisms (rs142984500 and rs4646116) typically found in Europeans which indicates a genetic susceptibility. This is amplified for Omicron (BA.1) and its sublineages BA.2 and BA.3. The antibody landscape was computationally investigated with the largest set of mAbs so far in the literature. From the 32 studied binders, groups of mAbs were identified from weak to strong binding affinities (e.g. S2K146). These mAbs with strong binding capacity and especially their combination are amenable to experimentation and clinical trials because of their high predicted binding affinities and possible neutralization potential for current known virus mutations and a universal coronavirus.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Carolina Corrêa Giron
- Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
- Universidade Federal do Triângulo Mineiro, Hospital de Clínicas, Uberaba, MG, Brazil
| | - Aatto Laaksonen
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
- State Key Laboratory of Materials-Oriented and Chemical Engineering, Nanjing Tech University, Nanjing, PR China
- Centre of Advanced Research in Bionanoconjugates and Biopolymers, Petru Poni Institute of Macromolecular Chemistry, Iasi, Romania
- Department of Engineering Sciences and Mathematics, Division of Energy Science, Luleå University of Technology, Luleå, Sweden
- Department of Chemical and Geological Sciences, University of Cagliari, Monserrato, Italy
| | - Fernando Luís Barroso da Silva
- Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| |
Collapse
|
4
|
Hossain A, Rahman ME, Rahman MS, Nasirujjaman K, Matin MN, Faruqe MO, Rabbee MF. Identification of medicinal plant-based phytochemicals as a potential inhibitor for SARS-CoV-2 main protease (M(pro)) using molecular docking and deep learning methods. Comput Biol Med 2023; 157:106785. [PMID: 36931201 DOI: 10.1016/j.compbiomed.2023.106785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 02/15/2023] [Accepted: 03/10/2023] [Indexed: 03/14/2023]
Abstract
Highly transmissive and rapidly evolving Coronavirus disease-2019 (COVID-19), a viral disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), triggered a global pandemic, which is one of the most researched viruses in the academia. Effective drugs to treat people with COVID-19 have yet to be developed to reduce mortality and transmission. Studies on the SARS-CoV-2 virus identified that its main protease (Mpro) might be a potential therapeutic target for drug development, as this enzyme plays a key role in viral replication. In search of potential inhibitors of Mpro, we developed a phytochemical library consisting of 2431 phytochemicals from 104 Korean medicinal plants that exhibited medicinal and antioxidant properties. The library was screened by molecular docking, followed by revalidation by re-screening with a deep learning method. Recurrent Neural Networks (RNN) computing system was used to develop an inhibitory predictive model using SARS coronavirus Mpro dataset. It was deployed to screen the top 12 compounds based on their docked binding affinity that ranged from -8.0 to -8.9 kcal/mol. The top two lead compounds, Catechin gallate and Quercetin 3-O-malonylglucoside, were selected depending on inhibitory potency against Mpro. Interactions with the target protein active sites, including His41, Met49, Cys145, Met165, and Thr190 were also examined. Molecular dynamics simulation was performed to analyze root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (RG), solvent accessible surface area (SASA), and number of hydrogen bonds. Results confirmed the inflexible nature of the docked complexes. Absorption, distribution, metabolism, excretion, and toxicity (ADMET), as well as bioactivity prediction confirmed the pharmaceutical activities of the lead compound. Findings of this research might help scientists to optimize compatible drugs for the treatment of COVID-19 patients.
Collapse
|
5
|
Hanai T. Further quantitative in silico analysis of SARS-CoV-2 S-RBD Omicron BA.4, BA.5, BA.2.75, BQ.1, and BQ.1.1 transmissibility. Talanta 2023; 254:124127. [PMID: 36462284 PMCID: PMC9682881 DOI: 10.1016/j.talanta.2022.124127] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/15/2022] [Accepted: 11/21/2022] [Indexed: 11/24/2022]
Abstract
The Covid-19 variants' transmissibility was further quantitatively analyzed in silico to study the binding strength with ACE-2 and find the binding inhibitors. The molecular interaction energy values of their optimized complex structures (MIFS) demonstrated that Omicron BA.4 and 5's MIFS value (344.6 kcal mol-1) was equivalent to wild-type MIFS (346.1 kcal mol-1), that of Omicron BQ.1 and BQ. 1.1's MIFS value (309.9 and 364.6 kcal mol-1). Furthermore, the MIFS value of Omicron BA.2.75 (515.1 kcal mol-1) was about Delta-plus (511.3 kcal mol-1). The binding strength of Omicron BA.4, BA. 5, and BQ.1.1 may be neglectable, but that of Omicron BA.2.75 was urging. Furthermore, the 79 medicine candidates were analyzed as the binding inhibitors from binding strength with ACE-2. Only carboxy compounds were repulsed from the ACE-2 binding site indicating that further modification of medical treatment candidates may produce an effective binding inhibitor.
Collapse
|
6
|
Kumar S, Choudhary M. New nickel( ii) Schiff base complexes as potential tools against SARS-CoV-2 Omicron target proteins: an in silico approach. NEW J CHEM 2023. [DOI: 10.1039/d2nj05136b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Herein, we report the in silico design and synthesis of two new nickel(ii) coordination complexes, based on Schiff bases derived from the 2-hydroxy-1-naphthaldehyde moiety.
Collapse
Affiliation(s)
- Sunil Kumar
- Department of Chemistry, National Institute of Technology Patna, Patna-800005, Bihar, India
| | - Mukesh Choudhary
- Department of Chemistry, National Institute of Technology Patna, Patna-800005, Bihar, India
| |
Collapse
|
7
|
Dhama K, Nainu F, Frediansyah A, Yatoo MI, Mohapatra RK, Chakraborty S, Zhou H, Islam MR, Mamada SS, Kusuma HI, Rabaan AA, Alhumaid S, Mutair AA, Iqhrammullah M, Al-Tawfiq JA, Mohaini MA, Alsalman AJ, Tuli HS, Chakraborty C, Harapan H. Global emerging Omicron variant of SARS-CoV-2: Impacts, challenges and strategies. J Infect Public Health 2023; 16:4-14. [PMID: 36446204 PMCID: PMC9675435 DOI: 10.1016/j.jiph.2022.11.024] [Citation(s) in RCA: 85] [Impact Index Per Article: 85.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/06/2022] [Accepted: 11/16/2022] [Indexed: 11/21/2022] Open
Abstract
Newly emerging variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are continuously posing high global public health concerns and panic resulting in waves of coronavirus disease 2019 (COVID-19) pandemic. Depending on the extent of genomic variations, mutations and adaptation, few of the variants gain the ability to spread quickly across many countries, acquire higher virulency and ability to cause severe disease, morbidity and mortality. These variants have been implicated in lessening the efficacy of the current COVID-19 vaccines and immunotherapies resulting in break-through viral infections in vaccinated individuals and recovered patients. Altogether, these could hinder the protective herd immunity to be achieved through the ongoing progressive COVID-19 vaccination. Currently, the only variant of interest of SARS-CoV-2 is Omicron that was first identified in South Africa. In this review, we present the overview on the emerging SARS-CoV-2 variants with a special focus on the Omicron variant, its lineages and hybrid variants. We discuss the hypotheses of the origin, genetic change and underlying molecular mechanism behind higher transmissibility and immune escape of Omicron variant. Major concerns related to Omicron including the efficacy of the current available immunotherapeutics and vaccines, transmissibility, disease severity, and mortality are discussed. In the last part, challenges and strategies to counter Omicron variant, its lineages and hybrid variants amid the ongoing COVID-19 pandemic are presented.
Collapse
Affiliation(s)
- Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India.
| | - Firzan Nainu
- Department of Pharmacy, Faculty of Pharmacy, Hasanuddin University, Makassar 90245, Indonesia
| | - Andri Frediansyah
- Research Division for Natural Product Technology (BPTBA), National Research and Innovation Agency (BRIN), Gunungkidul, Yogyakarta 55861, Indonesia
| | - Mohd Iqbal Yatoo
- Division of Veterinary Clinical Complex, Faculty of Veterinary Sciences and Animal Husbandry Shuhama, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu and Kashmir 190006, India
| | - Ranjan K Mohapatra
- Department of Chemistry, Government College of Engineering, Keonjhar 758002, Odisha, India
| | - Sandip Chakraborty
- Department of Veterinary Microbiology, College of Veterinary Sciences and Animal Husbandry, R.K. Nagar, West Tripura, Tripura, India
| | - Hao Zhou
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; Department of Microbiology, NYU Grossman School of Medicine, New York 10016, USA
| | - Md Rabiul Islam
- Department of Pharmacy, University of Asia Pacific, 74/A Green Road, Farmgate, Dhaka 1205, Bangladesh
| | - Sukamto S Mamada
- Department of Pharmacy, Faculty of Pharmacy, Hasanuddin University, Makassar 90245, Indonesia
| | - Hendrix Indra Kusuma
- Medical Research Unit, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Aceh 23111, Indonesia; Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Syiah Kuala, Banda Aceh 23111, Indonesia; Biology Education Department, Faculty of Tarbiyah and Teacher Training, Universitas Islam Negeri Ar-Raniry, Jl. Syeikh Abdur Rauf, Kopelma Darussalaml, Banda Aceh 23111, Indonesia
| | - Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan
| | - Saad Alhumaid
- Administration of Pharmaceutical Care, Al-Ahsa Health Cluster, Ministry of Health, Al-Ahsa 31982, Saudi Arabia
| | - Abbas Al Mutair
- Research Center, Almoosa Specialist Hospital, Al-Ahsa 36342, Saudi Arabia; College of Nursing, Prince Nora University, Riyadh 11564, Saudi Arabia; School of Nursing, Wollongong University, Wollongong, NSW 2522, Australia; Nursing Department, Prince Sultan Military College of Health Sciences, Dhahran 33048, Saudi Arabia
| | - Muhammad Iqhrammullah
- Graduate School of Mathematics and Applied Sciences, Universitas Syiah Kuala, Banda Aceh 23111, Indonesia
| | - Jaffar A Al-Tawfiq
- Specialty Internal Medicine and Quality Department, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia; Infectious Disease Division, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA; Infectious Disease Division, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mohammed Al Mohaini
- Basic Sciences Department, College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, Al-Ahsa 31982, Saudi Arabia; King Abdullah International Medical Research Center, Al-Ahsa 31982, Saudi Arabia
| | - Abdulkhaliq J Alsalman
- Department of Clinical Pharmacy, Faculty of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia
| | - Hardeep Singh Tuli
- Department of Biotechnology, Maharishi Markandeshwar University, Mullana, Ambala 133207, Haryana, India
| | - Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Barasat-Barrackpore Road, Kolkata, West Bengal 700126, India
| | - Harapan Harapan
- Medical Research Unit, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Aceh 23111, Indonesia; Tropical Diseases Centre, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Aceh 23111, Indonesia; Department of Microbiology, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Aceh 23111, Indonesia.
| |
Collapse
|
8
|
Feng L, Fu S, Zhang P, Zhang Y, Zhao Y, Yao Y, Luo L, Ping P. Potential use of the S-protein-Angiotensin converting enzyme 2 binding pathway in the treatment of coronavirus disease 2019. Front Public Health 2022; 10:1050034. [PMID: 36518573 PMCID: PMC9742547 DOI: 10.3389/fpubh.2022.1050034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/15/2022] [Indexed: 11/29/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the pathogen that causes coronavirus disease 2019 (COVID-19), infects humans through a strong interaction between the viral spike protein (S-protein) and angiotensin converting enzyme 2 (ACE2) receptors on the cell surface. The infection of host lung cells by SARS-CoV-2 leads to clinical symptoms in patients. However, ACE2 expression is not restricted to the lungs; altered receptors have been found in the nasal and oral mucosa, vessel, brain, pancreas, gastrointestinal tract, kidney, and heart. The future of COVID-19 is uncertain, however, new viral variants are likely to emerge. The SARS-CoV-2 Omicron variant has a total of 50 gene mutations compared with the original virus; 15 of which occur in the receptor binding domain (RBD). The RBD of the viral S-protein binds to the human ACE2 receptor for viral entry. Mutations of the ACE2-RBD interface enhance tight binding by increasing hydrogen bond interactions and expanding the accessible surface area. Extracorporeal membrane oxygenation, hyperbaric oxygen, and aggressive dialysis for the treatment of COVID-19 have shown various degrees of clinical success. The use of decoy receptors based on the ACE2 receptor as a broadly potent neutralizer of SARS-CoV-2 variants has potential as a therapeutic mechanism. Drugs such as 3E8 could block binding of the S1-subunit to ACE2 and restrict the infection of ACE2-expressing cells by a variety of coronaviruses. Here, we discuss the development of ACE2-targeted strategies for the treatment and prevention of COVID-19.
Collapse
Affiliation(s)
- Long Feng
- Department of Anesthesia, Hainan Hospital of Chinese People's Liberation Army General Hospital, Sanya, China
| | - Shihui Fu
- Department of Geriatric Cardiology, Chinese People's Liberation Army General Hospital, Beijing, China
- Department of Cardiology, Hainan Hospital of Chinese People's Liberation Army General Hospital, Sanya, China
| | - Pei Zhang
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Yujie Zhang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Yali Zhao
- Central Laboratory, Hainan Hospital of Chinese People's Liberation Army General Hospital, Sanya, China
| | - Yao Yao
- Center for Healthy Aging and Development Studies, National School of Development, Peking University, Beijing, China
| | - Leiming Luo
- Department of Geriatric Cardiology, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Ping Ping
- General Station for Drug and Instrument Supervision and Control, Joint Logistic Support Force of Chinese People's Liberation Army, Beijing, China
| |
Collapse
|
9
|
Zhou H, Møhlenberg M, Thakor JC, Tuli HS, Wang P, Assaraf YG, Dhama K, Jiang S. Sensitivity to Vaccines, Therapeutic Antibodies, and Viral Entry Inhibitors and Advances To Counter the SARS-CoV-2 Omicron Variant. Clin Microbiol Rev 2022; 35:e0001422. [PMID: 35862736 PMCID: PMC9491202 DOI: 10.1128/cmr.00014-22] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) keeps evolving and mutating into newer variants over time, which gain higher transmissibility, disease severity, and spread in communities at a faster rate, resulting in multiple waves of surge in Coronavirus Disease 2019 (COVID-19) cases. A highly mutated and transmissible SARS-CoV-2 Omicron variant has recently emerged, driving the extremely high peak of infections in almost all continents at an unprecedented speed and scale. The Omicron variant evades the protection rendered by vaccine-induced antibodies and natural infection, as well as overpowers the antibody-based immunotherapies, raising the concerns of current effectiveness of available vaccines and monoclonal antibody-based therapies. This review outlines the most recent advancements in studying the virology and biology of the Omicron variant, highlighting its increased resistance to current antibody-based therapeutics and its immune escape against vaccines. However, the Omicron variant is highly sensitive to viral fusion inhibitors targeting the HR1 motif in the spike protein, enzyme inhibitors, involving the endosomal fusion pathway, and ACE2-based entry inhibitors. Omicron variant-associated infectivity and entry mechanisms of Omicron variant are essentially distinct from previous characterized variants. Innate sensing and immune evasion of SARS-CoV-2 and T cell immunity to the virus provide new perspectives of vaccine and drug development. These findings are important for understanding SARS-CoV-2 viral biology and advances in developing vaccines, antibody-based therapies, and more effective strategies to mitigate the transmission of the Omicron variant or the next SARS-CoV-2 variant of concern.
Collapse
Affiliation(s)
- Hao Zhou
- Department of Microbiology, NYU Grossman School of Medicine, New York, New York, USA
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Michelle Møhlenberg
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Center for Cancer Biology, Department of Oncology, VIB-KU Leuven, Leuven, Belgium
| | - Jigarji C. Thakor
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Hardeep Singh Tuli
- Department of Biotechnology, Maharishi Markandeshwar (Deemed University), Mullana, Ambala, Haryana, India
| | - Pengfei Wang
- State Key Laboratory of Genetic Engineering, Shanghai Institute of Infectious Disease and Biosecurity, School of Life Sciences, Fudan University, Shanghai, China
| | - Yehuda G. Assaraf
- The Fred Wyszkowski Cancer Research Laboratory, Faculty of Biology, Technion Israel Institute of Technology, Haifa, Israel
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Fudan University, Shanghai, China
| |
Collapse
|
10
|
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: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
11
|
Sharma V, Rai H, Gautam DNS, Prajapati PK, Sharma R. Emerging evidence on Omicron (B.1.1.529) SARS-CoV-2 variant. J Med Virol 2022; 94:1876-1885. [PMID: 35083761 PMCID: PMC9015596 DOI: 10.1002/jmv.27626] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/19/2022] [Accepted: 01/22/2022] [Indexed: 11/24/2022]
Abstract
COVID's Omicron variant has sparked a slew of concerns across the globe. This review aims to provide a brief overview of what we know about the Omicron variant right now. The new variant has been discovered in 149 countries across all six World Health Organization (WHO) regions since its discovery in South Africa on November 24, 2021 and became the dominant variant in the country in less than 3 weeks. The WHO has warned that the B.1.1.529 variant is spreading at an unprecedented rate, and has urged countries to prepare for the worst. Over the course of this time, researchers from Africa and around the world have uncovered a wealth of information about the virus's epidemiology and biological properties. Case numbers are increasing exponentially in hard-hit areas such as South Africa, United Kingdom, and USA (overtaking the delta variant), implying that the variant is highly transmissible. Initial research has provided some insights into the efficacy of vaccines against the Omicron variant and whether it produces major illness, however, much remains unknown, and additional work is needed to investigate what the initial reports represent in real-world situations.
Collapse
Affiliation(s)
- Vineet Sharma
- Department of Rasa Shastra and Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical SciencesBanaras Hindu UniversityVaranasiIndia
| | - Himanshu Rai
- DST‐Centre for Interdisciplinary Mathematical Sciences, Institute of ScienceBanaras Hindu UniversityVaranasiIndia
| | - Dev N. S. Gautam
- Department of Rasa Shastra and Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical SciencesBanaras Hindu UniversityVaranasiIndia
| | - Pradeep K. Prajapati
- Department of Rasa Shastra and Bhaishajya KalpanaAll India Institute of AyurvedaNew DelhiIndia
| | - Rohit Sharma
- Department of Rasa Shastra and Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical SciencesBanaras Hindu UniversityVaranasiIndia
| |
Collapse
|
12
|
Liu JZ, Lv HC, Fu YJ, Cui Q. Amomum tsao-ko essential oil, a Novel Anti-COVID-19 Omircon Spike Protein Natural Products: A Computational Study. ARAB J CHEM 2022; 15:103916. [PMID: 35462797 PMCID: PMC9014638 DOI: 10.1016/j.arabjc.2022.103916] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 04/10/2022] [Indexed: 12/20/2022] Open
Abstract
Since the outbreak of COVID-19, this virus has been constantly mutating. The latest mutant Omicron has been identified as VOC by WHO. The main reason for its concern is the mutation of 46 amino acids in spike protein, which has brought the global epidemic prevention into another difficulty. Herbal aromatic plant Amomum tsao-ko was excavated from formula 1 and 2 for the treatment of COVID-19 in China, and its active components were extracted and identified. Molecular dynamics simulation and Fpocket were applied to find the key sites on RBDOmicron, and molecular docking was also used to reveal the interaction between A. tsao-ko essential oil (AEO) and RBDOmicron. The AEO components were analyzed and identified by GC/Q-TOF MS. There were 20 kinds of AEO with a relative area percentage of more than 1%, and they were related to the three active centres of RBDOmicron. In this study, virtual screening was used to mine the essential oil components of medicinal plants, and it was found that the components could interact with the spike protein RBD in aerosol to block the interaction of RBD and hACE2, thus cutting off the transmission route and protecting the host. This study has certain guiding significance in the modernization of Traditional Chinese medicine and the prevention of COVID-19.
Collapse
Affiliation(s)
- Ju-Zhao Liu
- College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou 311402, PR China
| | - Hong-Chang Lv
- School of Modern Post (School of Automation), Beijing University of Posts and Telecommunications, Beijing 100876, China
| | - Yu-Jie Fu
- College of Forestry, Beijing Forestry University, No. 35, Tsinghua East Road, Haidian District, Beijing 100083, PR China
| | - Qi Cui
- College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou 311402, PR China
| |
Collapse
|
13
|
Aloufi BH, Snoussi M, Sulieman AME. Antiviral Efficacy of Selected Natural Phytochemicals against SARS-CoV-2 Spike Glycoprotein Using Structure-Based Drug Designing. Molecules 2022; 27:2401. [PMID: 35458599 PMCID: PMC9025634 DOI: 10.3390/molecules27082401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 03/30/2022] [Accepted: 04/06/2022] [Indexed: 11/17/2022] Open
Abstract
SARS-CoV-2 is a highly virulent coronavirus that first surfaced in late 2019 and has since created a pandemic of the acute respiratory sickness known as “coronavirus disease 2019” (COVID-19), posing a threat to human health and public safety. S-RBD is a coronaviral protein that is essential for a coronavirus (CoV) to bind and penetrate into host cells. As a result, it has become a popular pharmacological target. The goal of this study was to find potential candidates for anti-coronavirus disease 2019 (COVID-19) drugs by targeting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) S-RBD with novel bioactive compounds and molecular interaction studies of 15,000 phytochemicals belonging to different flavonoid subgroups. A spike protein crystal structure attached to the ACE2 structure was obtained from the PDB database. A library of 15,000 phytochemicals was made by collecting compounds from different databases, such as the Zinc-database, PubChem-database, and MPD3-database. This library was docked against a receptor binding domain of a spike glycoprotein through the Molecular Operating Environment (MOE). The top drug candidates Phylloflavan, Milk thistle, Ilexin B and Isosilybin B, after virtual screening, were selected on the basis of the least binding score. Phylloflavan ranked as the top compound because of its least binding affinity score of −14.09 kcal/mol. In silico studies showed that all those compounds showed good activity and could be used as an immunological response with no bioavailability issues. Absorption, distribution, metabolism, excretion and a toxicological analysis were conducted through SwissADME. Stability and effectiveness of the docked complexes were elucidated by performing the 100 ns molecular dynamic simulation through the Desmond package.
Collapse
|
14
|
Vardhan S, Sahoo SK. Computational studies on the interaction of SARS-CoV-2 Omicron SGp RBD with human receptor ACE2, limonin and glycyrrhizic acid. Comput Biol Med 2022; 144:105367. [PMID: 35247766 PMCID: PMC8886687 DOI: 10.1016/j.compbiomed.2022.105367] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/25/2022] [Accepted: 02/28/2022] [Indexed: 01/06/2023]
Abstract
On November 24, 2021, the SARS-CoV-2 Omicron variant (B.1.1.529) was first identified in South Africa. The World Health Organization (WHO) declared the Omicron as a variant of concern (VoC) because of the unexpected and large numbers of mutations occurred in the genome, higher viral transmission and immune evasions. The present study was performed to explore the interactions of SARS-CoV-2 spike glycoprotein receptor-binding domain (SGp RBD) of the three variants (Omicron, Delta, and WT) with the receptor hACE2. The structural changes occurred in Omicron due to the mutations at key positions improved the ability to mediate SARS-CoV-2 viral infection compared to other VoCs. The phytochemicals limonin and glycyrrhizic acid were docked with the SGp RBD of the variants WT, Delta and Omicron. The computed dock score revealed that limonin and glycyrrhizic acid binds effectively at the SGp RBD of all three variants, and showed almost similar binding affinity at the binding interface of ACE2. Therefore, despite the multiple mutations occurred in Omicron and its viral transmission is comparatively high, the computed binding affinity of the phytochemicals limonin and glycyrrhizic acid supported that the traditional medicines can be useful in formulating adjuvant therapies to fight against the SARS-CoV-2 Omicron.
Collapse
Affiliation(s)
- Seshu Vardhan
- Department of Chemistry, Sardar Vallabhbhai National Institute of Technology (SVNIT), Surat, 395007, Gujarat, India
| | - Suban K Sahoo
- Department of Chemistry, Sardar Vallabhbhai National Institute of Technology (SVNIT), Surat, 395007, Gujarat, India.
| |
Collapse
|