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Article ; Online: Dock-able linear and homodetic di, tri, tetra and pentapeptide library from canonical amino acids: SARS-CoV-2 Mpro as a case study.

Ahmad, Sarfraz / Mirza, Muhammad Usman / Trant, John F

2023 Volume 13, Issue 5, Page(s) 523–534

Abstract: Peptide-based therapeutics are increasingly pushing to the forefront of biomedicine with their promise of high specificity and low toxicity. Although noncanonical residues can always be used, employing only the natural 20 residues restricts the chemical ... ...

Abstract	Peptide-based therapeutics are increasingly pushing to the forefront of biomedicine with their promise of high specificity and low toxicity. Although noncanonical residues can always be used, employing only the natural 20 residues restricts the chemical space to a finite dimension allowing for comprehensive in silico screening. Towards this goal, the dataset comprising all possible di-, tri-, and tetra-peptide combinations of the canonical residues has been previously reported. However, with increasing computational power, the comprehensive set of pentapeptides is now also feasible for screening as the comprehensive set of cyclic peptides comprising four or five residues. Here, we provide both the complete and prefiltered libraries of all di-, tri-, tetra-, and penta-peptide sequences from 20 canonical amino acids and their homodetic (N-to-C-terminal) cyclic homologues. The FASTA, simplified molecular-input line-entry system (SMILES), and structure-data file (SDF)-three dimension (3D) libraries can be readily used for screening against protein targets. We also provide a simple method and tool for conducting identity-based filtering. Access to this dataset will accelerate small peptide screening workflows and encourage their use in drug discovery campaigns. As a case study, the developed library was screened against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease to identify potential small peptide inhibitors.
Language	English
Publishing date	2023-04-15
Publishing country	China
Document type	Journal Article
ZDB-ID	2630174-X
ISSN	2214-0883 ; 2095-1779
ISSN (online)	2214-0883
ISSN	2095-1779
DOI	10.1016/j.jpha.2023.04.008
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Late-onset pulmonary complications among survivors of coronavirus Disease 2019.

Baig, Mirza Muhammad Ayub / Adnan, Muhammad / Baig, Muhammad Usman / Ramzan, Zohaib

Pakistan journal of medical sciences

2023 Volume 39, Issue 4, Page(s) 1035–1039

Abstract: Objectives: To assess the late-onset pulmonary complications among survivors of coronavirus disease 2019.: Methods: The cross-sectional analytical study was conducted in the department of Pulmonology, Sir Ganga Ram Hospital Lahore between October ... ...

Abstract	Objectives: To assess the late-onset pulmonary complications among survivors of coronavirus disease 2019. Methods: The cross-sectional analytical study was conducted in the department of Pulmonology, Sir Ganga Ram Hospital Lahore between October 2020 and March 2021. Total 288 patients visiting the hospital 12-week after recovery from COVID-19 enrolled using convenience sampling. After excluding patients (n=61) with a history of previous respiratory symptoms before the development of COVID-19, data from 227 patients was subjected to final analysis. Chest X-ray (CXR) was used to evaluate lung condition. Results: Participation of middle-aged adults (54.6%) was higher than older (38.3%) and young adults (7.0%). The percentage of males was 55.5% and smokers was 29.1%. Dyspnea was the most common complication as 80.0% patients had moderate to severe dyspnea while chronic cough was 78.0% and lung fibrosis (LF) was 13.2%. The chances of LF increased with the rise in age (p-value 0.033). However, the distribution of LF was similar between males and females. The frequency of lung fibrosis in smokers was 3-time higher than among non-smokers (24.2 vs. 8.7%; p-value 0.003). The patients with LF were more dependent on O2 as compared to the patients without LF (p-value < 0.001). The frequency of tachycardia was significantly different between patients with and without LF (all p-values < 0.05). Conclusion: LF is a common late-onset pulmonary complication of COVID-19 and is associated with old age, smoking, O
Language	English
Publishing date	2023-08-08
Publishing country	Pakistan
Document type	Journal Article
ZDB-ID	2032827-8
ISSN	1681-715X ; 1682-024X ; 1017-4699
ISSN (online)	1681-715X
ISSN	1682-024X ; 1017-4699
DOI	10.12669/pjms.39.4.6302
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Zs.A 3948: Show issues

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Article: Green bonds issuance, innovation performance, and corporate value: Empirical evidence from China.

Khurram, Muhammad Usman / Xie, Wenwu / Mirza, Sultan Sikandar / Tong, Hao

Heliyon

2023 Volume 9, Issue 4, Page(s) e14895

Abstract: This study investigates the impact of green bond issuance on corporate performance and further checks the intermediate effect of corporate innovation performance on the primary relationship. This study uses the quarterly panel data of Chinese non- ... ...

Abstract	This study investigates the impact of green bond issuance on corporate performance and further checks the intermediate effect of corporate innovation performance on the primary relationship. This study uses the quarterly panel data of Chinese non-financial listed companies in 11 subdivided industry categories from January 1, 2016, to September 30, 2020. Using the difference-in-difference (DID) model and the parallel trend test, it is found that companies' issuance of green bonds has a significant positive effect on improving corporate innovation performance and corporate value. Furthermore, the improvement of innovation performance assists in enhancing the promotion effect of green bond issuance on corporate value. Despite data limitations, this study's findings can be very helpful for all relevant stakeholders, especially regulators, to introduce conducive policies to support the issuance of green bonds in Chinese. Our findings can be useful for other emerging markets that are dealing with the same green bond-based growth-sustainability conundrum.
Language	English
Publishing date	2023-03-25
Publishing country	England
Document type	Journal Article
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2023.e14895
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Article ; Online: Green bonds issuance, innovation performance, and corporate value

Muhammad Usman Khurram / Wenwu Xie / Sultan Sikandar Mirza / Hao Tong

Heliyon, Vol 9, Iss 4, Pp e14895- (2023)

Empirical evidence from China

2023

Abstract	This study investigates the impact of green bond issuance on corporate performance and further checks the intermediate effect of corporate innovation performance on the primary relationship. This study uses the quarterly panel data of Chinese non-financial listed companies in 11 subdivided industry categories from January 1, 2016, to September 30, 2020. Using the difference-in-difference (DID) model and the parallel trend test, it is found that companies' issuance of green bonds has a significant positive effect on improving corporate innovation performance and corporate value. Furthermore, the improvement of innovation performance assists in enhancing the promotion effect of green bond issuance on corporate value. Despite data limitations, this study's findings can be very helpful for all relevant stakeholders, especially regulators, to introduce conducive policies to support the issuance of green bonds in Chinese. Our findings can be useful for other emerging markets that are dealing with the same green bond-based growth-sustainability conundrum.
Keywords	Green bonds ; Innovation performance ; Corporate value ; Emerging markets ; China ; Science (General) ; Q1-390 ; Social sciences (General) ; H1-99
Subject code	650
Language	English
Publishing date	2023-04-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
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Article: See Something, Say Something: Global Positioning System Tracker Foreign Body Ingestion as a Unique Presentation of Human Trafficking.

Mirza, Muhammad Usman / Jiang, Chunsu / Forde, Justin J / Barkin, Jodie A / Sussman, Daniel A / Manten, Emory M

ACG case reports journal

2024 Volume 11, Issue 3, Page(s) e01301

Abstract: In 2021, there were about 17,000 victims of human trafficking in the United States. We present a case of a 28-year-old sex trafficking victim who was forced to swallow 2 global positioning system trackers by her perpetrator. The gastroenterology team ... ...

Abstract	In 2021, there were about 17,000 victims of human trafficking in the United States. We present a case of a 28-year-old sex trafficking victim who was forced to swallow 2 global positioning system trackers by her perpetrator. The gastroenterology team performed an upper endoscopy and retrieved 2 global positioning system devices from her antrum. Most of these victims do not disclose any history of abuse because of fear of their perpetrators. Further training and research can help to allow for recognition of these victims and potentially help them.
Language	English
Publishing date	2024-03-16
Publishing country	United States
Document type	Case Reports
ZDB-ID	2814825-3
ISSN	2326-3253
ISSN	2326-3253
DOI	10.14309/crj.0000000000001301
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Article: Assessment of Generalized Joint Hypermobility and Its Association With Osteoarthritis, BMI, and Age: A Study in Southern Lahore.

Qamar, Muhammad Shaheer / Tahir, Malik Usman / Shehroz, Muhammad / Zameer, Anusha / Islam, Amil / Yousaf, Marya / Naseer, Nimra / Sikandar, Mirza Zeeshan

Cureus

2024 Volume 16, Issue 3, Page(s) e55990

Abstract: Background and objective: Joint hypermobility is a physiological variation in the joint range of motion that allows individuals to move their joints beyond the normal limit. Generalized joint hypermobility (GJH) refers to an increased flexibility ... ...

Abstract	Background and objective: Joint hypermobility is a physiological variation in the joint range of motion that allows individuals to move their joints beyond the normal limit. Generalized joint hypermobility (GJH) refers to an increased flexibility observed throughout various joints in the body. In younger individuals, joint hypermobility is often more pronounced, serving as a double-edged sword by providing enhanced flexibility for certain activities while simultaneously increasing the susceptibility to musculoskeletal issues. Weight gain and overactivity of joints (joint hypermobility) are associated with the onset of osteoarthritis (OA), and data for the local populace is lacking. This study aims to assess GJH and OA in young and middle-aged women in southern Lahore. Methodology: A cross-sectional study recruited 116 diagnosed OA patients through a random convenient sampling method. These patients were assessed for GJH using the Beighton criterion. For the assessment of GJH, the Beighton criterion was used, and for OA, radiographs of knee joints were taken. The Beighton criterion consists of nine movements, and each maneuver is assigned a score of either 0 or 1, resulting in a range from 0 to 9. A chi-square test was used for the group comparison of study variables. Results: A total of 116 adult females participated, with a mean age of 38.34 ± 9.761 and an age range of 20 to 55 years. GJH was assessed and correlated with age using the chi-square correlation and test. Results indicated that 78 (67.24%) exhibited hypermobility at various joint levels, with a likelihood ratio of 43.336 and a Conclusions: The dynamic nature of joint hypermobility emphasizes the need to consider age-related changes when assessing its impact on musculoskeletal health. Assessment and management of hypermobility in patients of OA, especially in females, should be made part of routine practices.
Language	English
Publishing date	2024-03-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	2747273-5
ISSN	2168-8184
ISSN	2168-8184
DOI	10.7759/cureus.55990
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Article ; Online: Structural elucidation of SARS-CoV-2 vital proteins: Computational methods reveal potential drug candidates against main protease, Nsp12 polymerase and Nsp13 helicase.

Mirza, Muhammad Usman / Froeyen, Matheus

Journal of pharmaceutical analysis

2020 Volume 10, Issue 4, Page(s) 320–328

Abstract: Recently emerged SARS-CoV-2 caused a major outbreak of coronavirus disease 2019 (COVID-19) and instigated a widespread fear, threatening global health safety. To date, no licensed antiviral drugs or vaccines are available against COVID-19 although ... ...

Abstract	Recently emerged SARS-CoV-2 caused a major outbreak of coronavirus disease 2019 (COVID-19) and instigated a widespread fear, threatening global health safety. To date, no licensed antiviral drugs or vaccines are available against COVID-19 although several clinical trials are under way to test possible therapies. During this urgent situation, computational drug discovery methods provide an alternative to tiresome high-throughput screening, particularly in the hit-to-lead-optimization stage. Identification of small molecules that specifically target viral replication apparatus has indicated the highest potential towards antiviral drug discovery. In this work, we present potential compounds that specifically target SARS-CoV-2 vital proteins, including the main protease, Nsp12 RNA polymerase and Nsp13 helicase. An integrative virtual screening and molecular dynamics simulations approach has facilitated the identification of potential binding modes and favourable molecular interaction profile of corresponding compounds. Moreover, the identification of structurally important binding site residues in conserved motifs located inside the active site highlights relative importance of ligand binding based on residual energy decomposition analysis. Although the current study lacks experimental validation, the structural information obtained from this computational study has paved way for the design of targeted inhibitors to combat COVID-19 outbreak.
Keywords	covid19
Language	English
Publishing date	2020-04-28
Publishing country	China
Document type	Journal Article
ZDB-ID	2630174-X
ISSN	2214-0883 ; 2095-1779
ISSN (online)	2214-0883
ISSN	2095-1779
DOI	10.1016/j.jpha.2020.04.008
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Article ; Online: Structural elucidation of SARS-CoV-2 vital proteins

Muhammad Usman Mirza / Matheus Froeyen

Journal of Pharmaceutical Analysis, Vol 10, Iss 4, Pp 320-

Computational methods reveal potential drug candidates against main protease, Nsp12 polymerase and Nsp13 helicase

2020 Volume 328

Abstract	Recently emerged SARS-CoV-2 caused a major outbreak of coronavirus disease 2019 (COVID-19) and instigated a widespread fear, threatening global health safety. To date, no licensed antiviral drugs or vaccines are available against COVID-19 although several clinical trials are under way to test possible therapies. During this urgent situation, computational drug discovery methods provide an alternative to tiresome high-throughput screening, particularly in the hit-to-lead-optimization stage. Identification of small molecules that specifically target viral replication apparatus has indicated the highest potential towards antiviral drug discovery. In this work, we present potential compounds that specifically target SARS-CoV-2 vital proteins, including the main protease, Nsp12 RNA polymerase and Nsp13 helicase. An integrative virtual screening and molecular dynamics simulations approach has facilitated the identification of potential binding modes and favourable molecular interaction profile of corresponding compounds. Moreover, the identification of structurally important binding site residues in conserved motifs located inside the active site highlights relative importance of ligand binding based on residual energy decomposition analysis. Although the current study lacks experimental validation, the structural information obtained from this computational study has paved way for the design of targeted inhibitors to combat COVID-19 outbreak.
Keywords	SARS-CoV-2 ; COVID-19 outbreak ; CoV-Mpro ; CoV-Nsp12 polymerase ; CoV-Nsp13 helicase ; Therapeutics. Pharmacology ; RM1-950 ; covid19
Subject code	540
Language	English
Publishing date	2020-08-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A novel missense compound heterozygous variant in TLR1 gene is associated with susceptibility to rheumatoid arthritis - structural perspective and functional annotations.

Pasha, Usman / Hanif, Kiran / Nisar, Haseeb / Abid, Rizwan / Mirza, Muhammad Usman / Wajid, Bilal / Sadaf, Saima

Clinical rheumatology

2023 Volume 42, Issue 11, Page(s) 3097–3111

Abstract: Introduction: Besides human leukocyte antigen (HLA-DRB1) locus, more than 100 loci across the genome have been identified and linked with the onset, expression and/or progression of rheumatoid arthritis (RA). However, there are still grey areas in our ... ...

Abstract	Introduction: Besides human leukocyte antigen (HLA-DRB1) locus, more than 100 loci across the genome have been identified and linked with the onset, expression and/or progression of rheumatoid arthritis (RA). However, there are still grey areas in our understanding of the key genetic contributors of the disease, particularly in familial cases. Methods: In the present study, we have performed the whole exome sequencing (WES) of RA patients from two consanguineous families of Pakistan in a quest to identify novel, high-impact, RA-susceptibility genetic variants. Results: Through stepwise filtering, around 17,000 variants (common in the affected members) were recognized, out of which 2651 were predicted to be deleterious. Of these, 196 had direct relevance to RA. When selected for homozygous recessive mode of inheritance, two novel pathogenic variants (c.1324T>C, p.Cys Conclusion: The results, validated through case-control study subjects, suggested that the variants identified through WES and confirmed through Sanger sequencing and MDS are the novel disease variants and are likely to confer RA-susceptibility, independently and/or in a family-specific context. Key Points • Exploration of population based/ethno-specific big data is imperative to identify novel causal variants of RA. • Two new deleterious missense mutations in mutational hotspot exon 4 of TLR1 gene have been identified in Pakistani RA patients. • MD simulation data provides evidence for domain's rigidification, conferring stability to mutant TLR1-TIR/TIRAP-TIR complex, with concomitant increase in production of pro-inflammatory cytokines, thus adding to the onset/erosive outcome of RA.
MeSH term(s)	Humans ; Arthritis, Rheumatoid/genetics ; Case-Control Studies ; Cytokines ; Genetic Predisposition to Disease ; Mutation, Missense ; Toll-Like Receptor 1/genetics
Chemical Substances	Cytokines ; Toll-Like Receptor 1 ; TLR1 protein, human
Language	English
Publishing date	2023-07-21
Publishing country	Germany
Document type	Journal Article
ZDB-ID	604755-5
ISSN	1434-9949 ; 0770-3198
ISSN (online)	1434-9949
ISSN	0770-3198
DOI	10.1007/s10067-023-06702-9
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Zs.A 1740: Show issues

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Article ; Online: Synthesis, biological evaluation, and molecular docking study of xanthene-linked thiosemicarbazones as cholinesterase inhibitors.

Naseem, Saira / Khan, Samra / Hussain, Safdar / Mirza, Muhammad Usman / Ashraf, Muhammad / Shafiq, Zahid / Trant, John F

Journal of biomolecular structure & dynamics

2023 , Page(s) 1–15

Abstract: This study delineates the design and synthesis of a series of xanthene-based thiosemicarbazones that show low μM inhibition of acetylcholinesterase (AChE) and butyrylcholinesterase (BChE), crucial enzymes associated with, among others, Alzheimer's ... ...

Abstract	This study delineates the design and synthesis of a series of xanthene-based thiosemicarbazones that show low μM inhibition of acetylcholinesterase (AChE) and butyrylcholinesterase (BChE), crucial enzymes associated with, among others, Alzheimer's Disease (AD) pathology. Despite FDA-approved AChE inhibitors being frontline treatments for AD, there remains a need for agents exhibiting improved efficacy and selectivity. Our synthesized series demonstrate meaningful inhibition against AChE (IC50 ranging from 4.2 to 62 μM). These compounds exhibit comparatively lower potency against BChE (IC50 values between 64 and 315 μM), showcasing a pronounced AChE selectivity compared to physostigmine. The selectivity index for the compounds between the two targets does vary between 0.02 and 0.75 highlighting that even minor structural differences can have drastic effects on protein interactions. Molecular docking insights further substantiated these observations, revealing the importance of the xanthene scaffold for AChE-binding and the aryl R
Language	English
Publishing date	2023-11-10
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2274981
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