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Article: Assessment of neutralization susceptibility of Omicron subvariants XBB.1.5 and BQ.1.1 against broad-spectrum neutralizing antibodies through epitopes mapping.

Shah, Masaud / Woo, Hyun Goo

2023 Volume 10, Page(s) 1236617

Abstract: The emergence of new variants of the SARS-CoV-2 virus has posed a significant challenge in developing broadly neutralizing antibodies (nAbs) with guaranteed therapeutic potential. Some nAbs, such as Sotrovimab, have exhibited varying levels of efficacy ... ...

Abstract	The emergence of new variants of the SARS-CoV-2 virus has posed a significant challenge in developing broadly neutralizing antibodies (nAbs) with guaranteed therapeutic potential. Some nAbs, such as Sotrovimab, have exhibited varying levels of efficacy against different variants, while others, such as Bebtelovimab and Bamlanivimab-etesevimab are ineffective against specific variants, including BQ.1.1 and XBB. This highlights the urgent need for developing broadly active monoclonal antibodies (mAbs) providing prophylactic and therapeutic benefits to high-risk patients, especially in the face of the risk of reinfection from new variants. Here, we aimed to investigate the feasibility of redirecting existing mAbs against new variants of SARS-CoV-2, as well as to understand how BQ.1.1 and XBB.1.5 can evade broadly neutralizing mAbs. By mapping epitopes and escape sites, we discovered that the new variants evade multiple mAbs, including FDA-approved Bebtelovimab, which showed resilience against other Omicron variants. Our approach, which included simulations, endpoint free energy calculation, and shape complementarity analysis, revealed the possibility of identifying mAbs that are effective against both BQ.1.1 and XBB.1.5. We identified two broad-spectrum mAbs, R200-1F9 and R207-2F11, as potential candidates with increased binding affinity to XBB.1.5 and BQ.1.1 compared to the reference (Wu01) strain. Additionally, we propose that these mAbs do not interfere with Angiotensin Converting Enzyme 2 (ACE2) and bind to conserved epitopes on the receptor binding domain of Spike that are not-overlapping, potentially providing a solution to neutralize these new variants either independently or as part of a combination (cocktail) treatment.
Language	English
Publishing date	2023-09-27
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2814330-9
ISSN	2296-889X
ISSN	2296-889X
DOI	10.3389/fmolb.2023.1236617
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Assessment of neutralization susceptibility of Omicron subvariants XBB.1.5 and BQ.1.1 against broad-spectrum neutralizing antibodies through epitopes mapping

Woo, Hyun Goo / Masaud, Shah

bioRxiv

Abstract	The emergence of new variants of the SARS-CoV-2 virus has posed a significant challenge in developing broadly neutralizing antibodies (nAbs) with guaranteed therapeutic potential. Some nAbs, such as Sotrovimab, have exhibited varying levels of efficacy against different variants, while others, such as Bebtelovimab and Bamlanivimab-etesevimab are ineffective against specific variants, including BQ.1.1 and XBB. This highlights the urgent need for developing broadly active mAbs providing prophylactic and therapeutic benefits to high-risk patients, especially in the face of the risk of reinfection from new variants. Here, we aimed to investigate the feasibility of redirecting existing mAbs against new variants of SARS-CoV-2, as well as to understand how BQ.1.1 and XBB.1.5 can evade broadly neutralizing mAbs. By mapping epitopes and escape sites, we discovered that the new variants evade multiple mAbs, including FDA-approved Bebtelovimab, which showed resilience against other Omicron variants. Our approach, which included simulations, free energy perturbations, and shape complementarity analysis, revealed the possibility of identifying mAbs that are effective against both BQ.1.1 and XBB.1.5. We identified two broad-spectrum mAbs, R200-1F9 and R207-2F11, as potential candidates with increased binding affinity to XBB.1.5 and BQ.1.1 compared to the wild-type virus. Additionally, we propose that these mAbs do not interfere with ACE2 and bind to conserved epitopes on the RBD that are not-overlapping, potentially providing a solution to neutralize these new variants either independently or as part of a combination (cocktail) treatment.
Keywords	covid19
Language	English
Publishing date	2023-03-02
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2023.03.01.530717
Database	COVID19

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Article ; Online: The paradigm of immune escape by SARS-CoV-2 variants and strategies for repositioning subverted mAbs against escaped VOCs.

Shah, Masaud / Woo, Hyun Goo

Molecular therapy : the journal of the American Society of Gene Therapy

2022 Volume 30, Issue 10, Page(s) 3101–3105

Abstract: The perpetual emergence of SARS-CoV-2 variants is a serious issue that makes it difficult for the therapeutic antibodies and vaccines to end the COVID-19 pandemic. This article discusses the trend of increasing host fitness and immune escape by the virus ...

Abstract	The perpetual emergence of SARS-CoV-2 variants is a serious issue that makes it difficult for the therapeutic antibodies and vaccines to end the COVID-19 pandemic. This article discusses the trend of increasing host fitness and immune escape by the virus and how to devise computational strategies for antibodies design and their affinity maturation against emerging SARS-CoV-2 variants.
MeSH term(s)	Antibodies, Monoclonal ; Antibodies, Neutralizing ; Antibodies, Viral ; COVID-19 ; Humans ; Neutralization Tests ; Pandemics ; SARS-CoV-2/genetics ; Spike Glycoprotein, Coronavirus ; Viral Envelope Proteins
Chemical Substances	Antibodies, Monoclonal ; Antibodies, Neutralizing ; Antibodies, Viral ; Spike Glycoprotein, Coronavirus ; Viral Envelope Proteins ; spike protein, SARS-CoV-2
Language	English
Publishing date	2022-09-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2010592-7
ISSN	1525-0024 ; 1525-0016
ISSN (online)	1525-0024
ISSN	1525-0016
DOI	10.1016/j.ymthe.2022.08.020
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Zs.A 5640: Show issues

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Article ; Online: Omicron: A Heavily Mutated SARS-CoV-2 Variant Exhibits Stronger Binding to ACE2 and Potently Escapes Approved COVID-19 Therapeutic Antibodies.

Shah, Masaud / Woo, Hyun Goo

Frontiers in immunology

2022 Volume 12, Page(s) 830527

Abstract: The new SARS-CoV-2 variant of concern "Omicron" was recently spotted in South Africa and spread quickly around the world due to its enhanced transmissibility. The variant became conspicuous as it harbors more than 30 mutations in the Spike protein with ... ...

Abstract	The new SARS-CoV-2 variant of concern "Omicron" was recently spotted in South Africa and spread quickly around the world due to its enhanced transmissibility. The variant became conspicuous as it harbors more than 30 mutations in the Spike protein with 15 mutations in the receptor-binding domain (RBD) alone, potentially dampening the potency of therapeutic antibodies and enhancing the ACE2 binding. More worrying, Omicron infections have been reported in vaccinees in South Africa and Hong Kong, and that post-vaccination sera poorly neutralize the new variant. Here, we investigated the binding strength of Omicron with ACE2 and monoclonal antibodies that are either approved by the FDA for COVID-19 therapy or undergoing phase III clinical trials. Computational mutagenesis and free energy perturbation could confirm that Omicron RBD binds ACE2 ~2.5 times stronger than prototype SARS-CoV-2. Notably, three substitutions, i.e., T478K, Q493K, and Q498R, significantly contribute to the binding energies and almost doubled the electrostatic potential (ELE) of the RBD
MeSH term(s)	Amino Acid Substitution ; Angiotensin-Converting Enzyme 2/chemistry ; Angiotensin-Converting Enzyme 2/genetics ; Angiotensin-Converting Enzyme 2/immunology ; Antibodies, Monoclonal/chemistry ; Antibodies, Monoclonal/immunology ; Antibodies, Monoclonal/therapeutic use ; Antibodies, Viral/chemistry ; Antibodies, Viral/immunology ; Antibodies, Viral/therapeutic use ; COVID-19/drug therapy ; COVID-19/genetics ; COVID-19/immunology ; Humans ; Immune Evasion ; Molecular Dynamics Simulation ; Mutation, Missense ; SARS-CoV-2/chemistry ; SARS-CoV-2/genetics ; SARS-CoV-2/immunology ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/immunology
Chemical Substances	Antibodies, Monoclonal ; Antibodies, Viral ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; ACE2 protein, human (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Language	English
Publishing date	2022-01-24
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2021.830527
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Article ; Online: Rational strategies for enhancing mAb binding to SARS-CoV-2 variants through CDR diversification and antibody-escape prediction.

Shah, Masaud / Shin, Ji-Yon / Woo, Hyun Goo

Frontiers in immunology

2023 Volume 14, Page(s) 1113175

Abstract: Since the emergence of SARS-CoV-2, dozens of variants of interest and half a dozen variants of concern (VOCs) have been documented by the World Health Organization. The emergence of these VOCs due to the continuous evolution of the virus is a major ... ...

Abstract	Since the emergence of SARS-CoV-2, dozens of variants of interest and half a dozen variants of concern (VOCs) have been documented by the World Health Organization. The emergence of these VOCs due to the continuous evolution of the virus is a major concern for COVID-19 therapeutic antibodies and vaccines because they are designed to target prototype/previous strains and lose effectiveness against new VOCs. Therefore, there is a need for time- and cost-effective strategies to estimate the immune escape and redirect therapeutic antibodies against newly emerging variants. Here, we computationally predicted the neutralization escape of the SARS-CoV-2 Delta and Omicron variants against the mutational space of RBD-mAbs interfaces. Leveraging knowledge of the existing RBD-mAb interfaces and mutational space, we fine-tuned and redirected CT-p59 (Regdanvimab) and Etesevimab against the escaped variants through complementarity-determining regions (CDRs) diversification. We identified antibodies against the Omicron lineage BA.1 and BA.2 and Delta variants with comparable or better binding affinities to that of prototype Spike. This suggests that CDRs diversification by hotspot grafting, given an existing insight into the Ag-Abs interface, is an exquisite strategy to redirect antibodies against preselected epitopes and combat the neutralization escape of emerging SARS-CoV-2 variants.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; COVID-19 ; Antibodies, Monoclonal/therapeutic use ; Complementarity Determining Regions/genetics
Chemical Substances	Antibodies, Monoclonal ; Complementarity Determining Regions
Language	English
Publishing date	2023-03-31
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2023.1113175
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Article ; Online: Molecular Perspectives of SARS-CoV-2: Pathology, Immune Evasion, and Therapeutic Interventions.

Shah, Masaud / Woo, Hyun Goo

Molecules and cells

2021 Volume 44, Issue 6, Page(s) 408–421

Abstract: The outbreak of coronavirus disease 2019 (COVID-19) has not only affected human health but also diverted the focus of research and derailed the world economy over the past year. Recently, vaccination against COVID-19 has begun, but further studies on ... ...

Abstract	The outbreak of coronavirus disease 2019 (COVID-19) has not only affected human health but also diverted the focus of research and derailed the world economy over the past year. Recently, vaccination against COVID-19 has begun, but further studies on effective therapeutic agents are still needed. The severity of COVID-19 is attributable to several factors such as the dysfunctional host immune response manifested by uncontrolled viral replication, type I interferon suppression, and release of impaired cytokines by the infected resident and recruited cells. Due to the evolving pathophysiology and direct involvement of the host immune system in COVID-19, the use of immune-modulating drugs is still challenging. For the use of immune-modulating drugs in severe COVID-19, it is important to balance the fight between the aggravated immune system and suppression of immune defense against the virus that causes secondary infection. In addition, the interplaying events that occur during virus-host interactions, such as activation of the host immune system, immune evasion mechanism of the virus, and manifestation of different stages of COVID-19, are disjunctive and require thorough streamlining. This review provides an update on the immunotherapeutic interventions implemented to combat COVID-19 along with the understanding of molecular aspects of the immune evasion of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which may provide opportunities to develop more effective and promising therapeutics.
MeSH term(s)	Antibodies, Monoclonal, Humanized/therapeutic use ; Antiviral Agents/therapeutic use ; COVID-19/immunology ; COVID-19/pathology ; COVID-19/prevention & control ; COVID-19/therapy ; COVID-19 Vaccines/administration & dosage ; Clinical Trials as Topic ; Cytokines/antagonists & inhibitors ; Cytokines/biosynthesis ; Dexamethasone/therapeutic use ; Drug Combinations ; Humans ; Immune Evasion/drug effects ; Immunity, Innate/drug effects ; Immunization, Passive/methods ; Immunologic Factors/therapeutic use ; Interleukin 1 Receptor Antagonist Protein/therapeutic use ; Peptides/therapeutic use ; SARS-CoV-2/drug effects ; SARS-CoV-2/immunology ; SARS-CoV-2/pathogenicity ; Virus Replication/drug effects ; Virus Replication/immunology ; COVID-19 Serotherapy
Chemical Substances	Antibodies, Monoclonal, Humanized ; Antiviral Agents ; COVID-19 Vaccines ; Cytokines ; Drug Combinations ; Immunologic Factors ; Interleukin 1 Receptor Antagonist Protein ; Peptides ; casirivimab and imdevimab drug combination ; Dexamethasone (7S5I7G3JQL)
Language	English
Publishing date	2021-05-31
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	1148964-9
ISSN	0219-1032 ; 1016-8478
ISSN (online)	0219-1032
ISSN	1016-8478
DOI	10.14348/molcells.2021.0026
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Zs.A 4713: Show issues

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ab Jg. 2022: Lesesaal (EG)

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Article ; Online: Differential glycosylation in mutant vitamin D-binding protein decimates the binding stability of vitamin D.

Usama / Khan, Zahid / Ali, Aktar / Shah, Masaud / Imran, Muhammad

Journal of biomolecular structure & dynamics

2023 , Page(s) 1–11

Abstract: Vitamin D (VD) is produced by the skin upon exposure to sunlight or is obtained from dietary sources. Several risk factors are associated with VD deficiency including mutations and post-translational modifications in its transport protein known as ... ...

Abstract	Vitamin D (VD) is produced by the skin upon exposure to sunlight or is obtained from dietary sources. Several risk factors are associated with VD deficiency including mutations and post-translational modifications in its transport protein known as vitamin D binding protein (VDBP) or GC-globulin. The two common single nucleotide polymorphisms rs7041 and rs4588 create three major isoforms of VDBP, including GC-1F also called wild type, GC1S, and GC-2. The 3D models for both GC-1F and GC-2 were constructed in their glycosylated states to decipher the effect of these mutations on the overall conformational changes and VD-binding affinity. The binding affinities were estimated using the Molecular Mechanics Poison-Boltzmann surface area (MM-PBSA) method and conformational changes were investigated after free energy landscapes estimations. Total free energies suggest that GC-1F exhibits stronger affinity (ΔE = -116.09 kJ/mol) than GC-2 (ΔE = -95 kJ/mol) variant with VD. The GC-1F isoforms had more streamlined motion compared to GC-2 isoforms, predicting a trade-off between cross-talk residues that significantly impacts protein structural stability. The data suggest that glycation at Thr418 plays a vital role in the overall VDBP-VD affinity by stabilizing the N-T loop that holds the domain I (VD-pocket) and domain III intact. The loss of glycation in GC-2 has a pivotal role in the inter-domain conformational stability of VDBP, which may ultimately affect VD transportation and maturation. These findings describe a novel mechanism in how mutations distant from the VD-active site change the overall conformational of the VDBP and abrogate the VDBP-VD interaction.Communicated by Ramaswamy H. Sarma.
Language	English
Publishing date	2023-06-25
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2226742
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Zs.A 2093: Show issues

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Article ; Online: Analysis of dataset on reduction of high temperature stress by green net shade alleviate oxidative stress and augments the growth and vase life of gladiolus cut flower.

Qayyum, Muhammad Mazhar / Hassan, Imran / Khan, Shah Masaud / Subhan, Mishal / Saleem, Shahzad / Fiaz, Sajid / Alharbi, Sulaiman Ali / Ansari, Mohammad Javed

Data in brief

2024 Volume 54, Page(s) 110378

Abstract: The study was conducted to investigate the effect of green net shade during staggered planting times on growth, biochemical, antioxidant enzymes and vase life of gladiolus cut flowers. The green net shade effectively reduces the internal temperature, ... ...

Abstract	The study was conducted to investigate the effect of green net shade during staggered planting times on growth, biochemical, antioxidant enzymes and vase life of gladiolus cut flowers. The green net shade effectively reduces the internal temperature, particularly during extremely hot planting times. Under the green net shade conditions, high quality morphological and biochemical observations were observed during the months of March and April planting times. These included longer plant height, spike length, a higher number of leaves plant
Language	English
Publishing date	2024-04-05
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2786545-9
ISSN	2352-3409 ; 2352-3409
ISSN (online)	2352-3409
ISSN	2352-3409
DOI	10.1016/j.dib.2024.110378
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Article ; Online: Regulatory pathways and therapeutic potential of PDE4 in liver pathophysiology.

Zahra, Noureen / Rafique, Shazia / Naveed, Zoya / Nadeem, Jannat / Waqas, Muhammad / Ali, Amjad / Shah, Masaud / Idrees, Muhammad

Life sciences

2024 Volume 345, Page(s) 122565

Abstract: Phosphodiesterase 4 (PDE4), crucial in regulating the cyclic adenosine monophosphate (cAMP) signaling pathway, significantly impacts liver pathophysiology. This article highlights the comprehensive effects of PDE4 on liver health and disease, and its ... ...

Abstract	Phosphodiesterase 4 (PDE4), crucial in regulating the cyclic adenosine monophosphate (cAMP) signaling pathway, significantly impacts liver pathophysiology. This article highlights the comprehensive effects of PDE4 on liver health and disease, and its potential as a therapeutic agent. PDE4's role in degrading cAMP disrupts intracellular signaling, increasing pro-inflammatory cytokines like tumor necrosis factor-alpha (TNF-α) and interleukin-6 (IL-6). This contributes to liver inflammation in conditions such as hepatitis and non-alcoholic steatohepatitis (NASH). Additionally, PDE4 is a key factor in liver fibrosis, characterized by excessive extracellular matrix deposition. Inhibiting PDE4 shows promise in reducing liver fibrosis by decreasing the activation of hepatic stellate cells, which is pivotal in fibrogenesis. PDE4 also influences hepatocyte apoptosis a common feature of liver diseases. PDE4 inhibitors protect against hepatocyte apoptosis by raising intracellular cAMP levels, thus activating anti-apoptotic pathways. This suggests potential in targeting PDE4 to prevent hepatocyte loss. Moreover, PDE4 regulates hepatic glucose production and lipid metabolism, essential for liver function. Altering cAMP levels through PDE4 affects enzymes in these metabolic pathways, making PDE4 a target for metabolic disorders like type 2 diabetes and non-alcoholic fatty liver disease (NAFLD). Since PDE4 plays a multifaceted role in liver pathophysiology, influencing PDE4's mechanisms in liver diseases could lead to novel therapeutic strategies. Still, extensive research is required to explore the molecular mechanisms and clinical potential of targeting PDE4 in liver pathologies.
MeSH term(s)	Humans ; Cyclic Nucleotide Phosphodiesterases, Type 4/metabolism ; Diabetes Mellitus, Type 2/metabolism ; Hepatitis/metabolism ; Hepatitis/pathology ; Liver/metabolism ; Liver/pathology ; Liver Cirrhosis/metabolism ; Liver Cirrhosis/pathology ; Non-alcoholic Fatty Liver Disease/metabolism
Chemical Substances	Cyclic Nucleotide Phosphodiesterases, Type 4 (EC 3.1.4.17) ; PDE4A protein, human (EC 3.1.4.17)
Language	English
Publishing date	2024-03-21
Publishing country	Netherlands
Document type	Journal Article ; Review
ZDB-ID	3378-9
ISSN	1879-0631 ; 0024-3205
ISSN (online)	1879-0631
ISSN	0024-3205
DOI	10.1016/j.lfs.2024.122565
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Uc I Zs.368: Show issues

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Article: SARS-CoV-2 pan-variant inhibitory peptides deter S1-ACE2 interaction and neutralize delta and omicron pseudoviruses.

Shah, Masaud / Ung Moon, Sung / Hyun Kim, Jang / Thanh Thao, Trinh / Goo Woo, Hyun

Computational and structural biotechnology journal

2022 Volume 20, Page(s) 2042–2056

Abstract: Approved neutralizing antibodies that target the prototype Spike are losing their potency against the emerging variants of concern (VOCs) of SARS-CoV-2, particularly Omicron. Although SARS-CoV-2 is continuously adapting the host environment, emerging ... ...

Abstract	Approved neutralizing antibodies that target the prototype Spike are losing their potency against the emerging variants of concern (VOCs) of SARS-CoV-2, particularly Omicron. Although SARS-CoV-2 is continuously adapting the host environment, emerging variants recognize the same ACE2 receptor for cell entry. Protein and peptide decoys derived from ACE2 or Spike proteins may hold the pan-variant inhibitory potential. Here, we deployed interactive structure- and pharmacophore-based approaches to design short and stable peptides
Language	English
Publishing date	2022-04-26
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2694435-2
ISSN	2001-0370
ISSN	2001-0370
DOI	10.1016/j.csbj.2022.04.030
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