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Article ; Online: Structure-based identification of novel inhibitors targeting the enoyl-ACP reductase enzyme of Acinetobacter baumannii

Shama Khan / Shabir A. Madhi / Courtney Olwagen

Scientific Reports, Vol 13, Iss 1, Pp 1-

2023 Volume 12

Abstract: Abstract Acinetobacter baumannii is a Gram-negative multidrug-resistant bacterial pathogen primarily associated with nosocomial infections resulting in increased morbidity and mortality in adults and infants, especially in sub-Saharan Africa where the ... ...

Abstract	Abstract Acinetobacter baumannii is a Gram-negative multidrug-resistant bacterial pathogen primarily associated with nosocomial infections resulting in increased morbidity and mortality in adults and infants, especially in sub-Saharan Africa where the clinical burden is high. New therapeutics are needed to treat multidrug-resistant Acinetobacter baumannii infections and reduce transmission. The study used computer-integrated drug discovery approaches including pharmacophore modelling, molecular docking, and molecular dynamics simulation to screen potential inhibitors against the enoyl-acyl carrier protein reductase—FabI protein of Acinetobacter baumannii. The top three potential inhibitors: 21272541 > 89795992 > 89792657 showed favourable binding free energies including coulombic energy, van der Waals energy, and polar and non-polar energies. Furthermore, all three complexes were extremely stable and compact with reduced fluctuations during the simulations period. Inhibitor 21272541 exhibited the highest binding affinity against the Acinetobacter baumannii FabI protein. This is similar to our recent report, which also identified 21272541 as the lead inhibitor against Klebsiella pneumoniae infections. Future clinical studies evaluating drug effectiveness should prioritise inhibitor 21272541 which could be effective in treating infections caused by Gram-negative organisms.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2023-12-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: ABBV-744 as a potential inhibitor of SARS-CoV-2 main protease enzyme against COVID-19

Zeynab Fakhar / Shama Khan / Suliman Y. AlOmar / Afrah Alkhuriji / Aijaz Ahmad

Scientific Reports, Vol 11, Iss 1, Pp 1-

2021 Volume 15

Abstract: Abstract A new pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide and become pandemic with thousands new deaths and infected cases globally. To address coronavirus disease (COVID-19), currently no effective drug or ...

Abstract	Abstract A new pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide and become pandemic with thousands new deaths and infected cases globally. To address coronavirus disease (COVID-19), currently no effective drug or vaccine is available. This necessity motivated us to explore potential lead compounds by considering drug repurposing approach targeting main protease (Mpro) enzyme of SARS-CoV-2. This enzyme considered to be an attractive drug target as it contributes significantly in mediating viral replication and transcription. Herein, comprehensive computational investigations were performed to identify potential inhibitors of SARS-CoV-2 Mpro enzyme. The structure-based pharmacophore modeling was developed based on the co-crystallized structure of the enzyme with its biological active inhibitor. The generated hypotheses were applied for virtual screening based PhaseScore. Docking based virtual screening workflow was used to generate hit compounds using HTVS, SP and XP based Glide GScore. The pharmacological and physicochemical properties of the selected lead compounds were characterized using ADMET. Molecular dynamics simulations were performed to explore the binding affinities of the considered lead compounds. Binding energies revealed that compound ABBV-744 binds to the Mpro with strong affinity (ΔG bind −45.43 kcal/mol), and the complex is more stable in comparison with other protein–ligand complexes. Our study classified three best compounds which could be considered as promising inhibitors against main protease SARS-CoV-2 virus.
Keywords	Medicine ; R ; Science ; Q
Subject code	540
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Investigating single amino acid substitutions in PIM1 kinase

Alaa Shafie / Shama Khan / Sagar Batra / Farah Anjum / Taj Mohammad / Shoaib Alam / Dharmendra Kumar Yadav / Asimul Islam / Md Imtaiyaz Hassan

PLoS ONE, Vol 16, Iss 10, p e

A structural genomics approach.

2021 Volume 0258929

Abstract: PIM1, is a serine/threonine proto-oncogene kinase, involved in many biological functions, including cell survival, proliferation, and differentiation, thus play a key role in oncogenesis. It plays a crucial role in the onset and progression of various ... ...

Abstract	PIM1, is a serine/threonine proto-oncogene kinase, involved in many biological functions, including cell survival, proliferation, and differentiation, thus play a key role in oncogenesis. It plays a crucial role in the onset and progression of various hematopoietic and non-hematopoietic malignancies, including acute myeloid leukemia and prostate cancer. Mutations in PIM1, especially in its kinase domain, can induce abnormal structural changes and thus alter functionalities that can lead to disease progression and other complexities. Herein, we have performed an extensive analysis of the PIM1 mutations at sequence and structure level while utilizing state-of-the-art computational approaches. Based on the impact on PIM1, numerous pathogenic and destabilizing mutations were identified and subsequently analyzed in detail. Finally, two amino acid substitutions (W109C and F147C) in the kinase domain of PIM1 were selected to explore their impact on the PIM1 structure in a time evolution manner using all-atom molecular dynamics (MD) simulations for 200 ns. MD results indicate significant conformational altercations in the structure of PIM1, especially upon F147C mutation. This study provides a significant insight into the PIM1 dysfunction upon single amino acid substitutions, which can be utilized to get insights into the molecular basis of PIM1-associated disease progression.
Keywords	Medicine ; R ; Science ; Q
Subject code	500
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Investigating single amino acid substitutions in PIM1 kinase

Alaa Shafie / Shama Khan / Sagar Batra / Farah Anjum / Taj Mohammad / Shoaib Alam / Dharmendra Kumar Yadav / Asimul Islam / Md. Imtaiyaz Hassan

PLoS ONE, Vol 16, Iss

A structural genomics approach

2021 Volume 10

Abstract	PIM1, is a serine/threonine proto-oncogene kinase, involved in many biological functions, including cell survival, proliferation, and differentiation, thus play a key role in oncogenesis. It plays a crucial role in the onset and progression of various hematopoietic and non-hematopoietic malignancies, including acute myeloid leukemia and prostate cancer. Mutations in PIM1, especially in its kinase domain, can induce abnormal structural changes and thus alter functionalities that can lead to disease progression and other complexities. Herein, we have performed an extensive analysis of the PIM1 mutations at sequence and structure level while utilizing state-of-the-art computational approaches. Based on the impact on PIM1, numerous pathogenic and destabilizing mutations were identified and subsequently analyzed in detail. Finally, two amino acid substitutions (W109C and F147C) in the kinase domain of PIM1 were selected to explore their impact on the PIM1 structure in a time evolution manner using all-atom molecular dynamics (MD) simulations for 200 ns. MD results indicate significant conformational altercations in the structure of PIM1, especially upon F147C mutation. This study provides a significant insight into the PIM1 dysfunction upon single amino acid substitutions, which can be utilized to get insights into the molecular basis of PIM1-associated disease progression.
Keywords	Medicine ; R ; Science ; Q
Subject code	500
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: An unusual case of haemoperitonium and bladder invasion due to placenta percreta in the third trimester mimicking threatened uterine rupture

Shama Khan / Kavita N. Singh / Vineeta Ghanghoriya

International Journal of Reproduction, Contraception, Obstetrics and Gynecology, Vol 5, Iss 2, Pp 556-

2016 Volume 558

Abstract: Placenta praevia percreta is a rare but potentially lethal complication of pregnancy. It has an increasing clinical significance due to its association with previous caesarian section and uterine curettage. Herein we report a patient with placenta ... ...

Abstract	Placenta praevia percreta is a rare but potentially lethal complication of pregnancy. It has an increasing clinical significance due to its association with previous caesarian section and uterine curettage. Herein we report a patient with placenta percreta, presenting in the emergency as 33 weeks of gestation with acute pain in abdomen and haemorrhagic shock, mimicking silent spontaneous uterine rupture, managed by emergency caesarian section followed by cesarian hysterectomy and bladder repair. [Int J Reprod Contracept Obstet Gynecol 2016; 5(2.000): 556-558]
Keywords	Percreta ; Hemoperitonium ; Bladder invasion ; Gynecology and obstetrics ; RG1-991 ; Medicine ; R
Language	English
Publishing date	2016-02-01T00:00:00Z
Publisher	Medip Academy
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Tracing Potential Covalent Inhibitors of an E3 Ubiquitin Ligase through Target-Focused Modelling

Imane Bjij / Pritika Ramharack / Shama Khan / Driss Cherqaoui / Mahmoud E. S. Soliman

Molecules, Vol 24, Iss 17, p

2019 Volume 3125

Abstract: The Nedd4-1 E3 Ubiquitin ligase has been implicated in multiple disease conditions due its overexpression. Although the enzyme may be targeted both covalently and non-covalently, minimal studies provide effective inhibitors against it. Recently, research ...

Abstract	The Nedd4-1 E3 Ubiquitin ligase has been implicated in multiple disease conditions due its overexpression. Although the enzyme may be targeted both covalently and non-covalently, minimal studies provide effective inhibitors against it. Recently, research has focused on covalent inhibitors based on their characteristic, highly-selective warheads and ability to prevent drug resistance. This prompted us to screen for new covalent inhibitors of Nedd4-1 using a combination of computational approaches. However, this task proved challenging due to the limited number of electrophilic moieties available in virtual libraries. Therefore, we opted to divide an existing covalent Nedd4-1 inhibitor into two parts: a non-covalent binding group and a pre-selected α, β-unsaturated ester that forms the covalent linkage with the protein. A non-covalent pharmacophore model was built based on molecular interactions at the binding site. The pharmacophore was then subjected to virtual screening to identify structurally similar hit compounds. Multiple filtrations were implemented prior to selecting four hits, which were validated with a covalent conjugation and later assessed by molecular dynamic simulations. The results showed that, of the four hit molecules, Zinc00937975 exhibited advantageous molecular groups, allowing for favourable interactions with one of the characteristic cysteine residues. Predictive pharmacokinetic analysis further justified the compound as a potential lead molecule, prompting its recommendation for confirmatory biological evaluation. Our inhouse, refined, pharmacophore model approach serves as a robust method that will encourage screening for novel covalent inhibitors in drug discovery.
Keywords	covalent inhibition ; NEDD4-1 E3 ligase ; molecular modeling ; pharmacophore modeling ; molecular dynamic simulations ; Organic chemistry ; QD241-441
Subject code	540
Language	English
Publishing date	2019-08-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Insight into maternal mortality of tertiary referral hospital of Madhya Pradesh

Bharti Sahu / Padma Shukla / Shama Khan / Parwati Sharma

International Journal of Reproduction, Contraception, Obstetrics and Gynecology, Vol 4, Iss 5, Pp 1339-

destination far ahead

2015 Volume 1343

Abstract: Background: Demise of mother wreaks havoc in family, society and ultimately nation. Amongst so many countries, India alone contributes one quarter of total world maternal deaths. Millennium Development Goal targeted to cut down maternal mortality up to ... ...

Abstract	Background: Demise of mother wreaks havoc in family, society and ultimately nation. Amongst so many countries, India alone contributes one quarter of total world maternal deaths. Millennium Development Goal targeted to cut down maternal mortality up to or less than 109 per lakh of total live births is far away from present level prevailing especially in our institution of Madhya Pradesh in centre of India. Methods: A retrospective analysis of maternal deaths from hospital records and death summaries of one year between Jan 2014 to Dec 2014 at NSCB Medical College and Hospital, Jabalpur in Madhya Pradesh. Results: During the review period, there were 75 maternal deaths and 5509 live births. (Institutional maternal mortality ratio, 1361.1 per lakh live births). All cases were analysed in detail: 70.6% (n = 53) were direct maternal deaths and PIH (n = 34, 45.33%) and Haemorrhage and sepsis (n = 7, 9.33%) were the leading causes of mortality. In indirect causes 29.33% (n = 22), severe anaemia topped (n=14, 18.66%). Women frequently did not attend prenatal clinics (n = 73, 97.33%),were resident of rural areas (n = 67, 89.33%) , referred (n = 68 , 90.66% ) most of them were of age of 20-30 years ( n=64, 82%) primigravida ( n = 45 , 60%),70% postnatal and experienced delays in care (n = 41 ,44.66%) and lost battle of life within 24 hrs. of admission. Conclusions: The burden of maternal mortality was found to be unacceptably high. Most women died of direct causes and experienced delays in care. Improvement in the quality of skilled maternity care, utmost need to avail good, proper and effective antenatal care, timely referral, prompt transportation, provision of family planning services, among other factors, can drastically curtail the maternal deaths. [Int J Reprod Contracept Obstet Gynecol 2015; 4(5.000): 1339-1343]
Keywords	Maternal mortality ; Antenatal care ; Emoc ; MDG ; Gynecology and obstetrics ; RG1-991 ; Medicine ; R
Language	English
Publishing date	2015-10-01T00:00:00Z
Publisher	Medip Academy
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Impact of Deleterious Mutations on Structure, Function and Stability of Serum/Glucocorticoid Regulated Kinase 1

Mohamed F. AlAjmi / Shama Khan / Arunabh Choudhury / Taj Mohammad / Saba Noor / Afzal Hussain / Wenying Lu / Mathew Suji Eapen / Vrushali Chimankar / Philip M Hansbro / Sukhwinder Singh Sohal / Abdelbaset Mohamed Elasbali / Md. Imtaiyaz Hassan

Frontiers in Molecular Biosciences, Vol

A Gene to Diseases Correlation

2021 Volume 8

Abstract: Serum and glucocorticoid-regulated kinase 1 (SGK1) is a Ser/Thr protein kinase involved in regulating cell survival, growth, proliferation, and migration. Its elevated expression and dysfunction are reported in breast, prostate, hepatocellular, lung ... ...

Abstract	Serum and glucocorticoid-regulated kinase 1 (SGK1) is a Ser/Thr protein kinase involved in regulating cell survival, growth, proliferation, and migration. Its elevated expression and dysfunction are reported in breast, prostate, hepatocellular, lung adenoma, and renal carcinomas. We have analyzed the SGK1 mutations to explore their impact at the sequence and structure level by utilizing state-of-the-art computational approaches. Several pathogenic and destabilizing mutations were identified based on their impact on SGK1 and analyzed in detail. Three amino acid substitutions, K127M, T256A, and Y298A, in the kinase domain of SGK1 were identified and incorporated structurally into original coordinates of SGK1 to explore their time evolution impact using all-atom molecular dynamic (MD) simulations for 200 ns. MD results indicate substantial conformational alterations in SGK1, thus its functional loss, particularly upon T256A mutation. This study provides meaningful insights into SGK1 dysfunction upon mutation, leading to disease progression, including cancer, and neurodegeneration.
Keywords	serum/glucocorticoid regulated kinase 1 ; deleterious mutations ; single amino acid substitutions ; molecular dynamics simulation ; essential dynamics ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2021-11-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Dystocia Due to Relative Oversized Fetus and fetal maldisposition in a Buffalo

Navneet Vasishta / Amit Sharma / Pravesh Kumar / Shama Khan / Purabi Barman

Veterinary World, Vol 4, Iss 12.000, Pp 569-

2011 Volume 570

Abstract: A primiparous Murrah graded buffalo suffering with dystocia due to relative oversize fetus and fetal maldisposition and its successful management following laparohysterotomy has been described. [Vet. World 2011; 4(12.000): 569-570] ...

Abstract	A primiparous Murrah graded buffalo suffering with dystocia due to relative oversize fetus and fetal maldisposition and its successful management following laparohysterotomy has been described. [Vet. World 2011; 4(12.000): 569-570]
Keywords	Dystocia ; Fetal maldisposition ; Obstetric ; Buffalo ; Oversized Fetus ; Animal culture ; SF1-1100 ; Veterinary medicine ; SF600-1100
Language	English
Publishing date	2011-01-01T00:00:00Z
Publisher	Veterinary World
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Evaluation of Maxwell® 16 for automated DNA extraction from whole blood and formalin-fixed paraffin embedded (FFPE) tissue.

Khokhar, Shama Khan / Mitui, Midori / Leos, Nora Kristine / Rogers, Beverly Barton / Park, Jason Y

Clinical chemistry and laboratory medicine

2011 Volume 50, Issue 2, Page(s) 267–272

Abstract: Background: The aim of the study was to assess the performance of Promega, Maxwell® 16 for the extraction of genomic DNA from whole blood and FFPE tissue.: Methods: DNA was extracted from 10 whole blood and 10 FFPE specimens using six different ... ...

Abstract	Background: The aim of the study was to assess the performance of Promega, Maxwell® 16 for the extraction of genomic DNA from whole blood and FFPE tissue. Methods: DNA was extracted from 10 whole blood and 10 FFPE specimens using six different commercial kits. Results: For whole blood, the mean DNA concentration obtained by Maxwell® 16 was significantly greater than either easyMAG® (p<0.0001) or QIAamp® Blood DNA kit (p<0.001). For FFPE, the mean DNA concentration obtained by the AllPrep® FFPE specific DNA/RNA kit was significantly greater than either the Maxwell® 16 (p<0.0001) or the general AllPrep® DNA/RNA kit (p<0.0001). Conclusions: Comparative evaluation of the six DNA extraction kits indicated that the semi-automated Maxwell® 16 was superior for whole blood extraction while the manual AllPrep® FFPE DNA/RNA kit (Qiagen) performed better for FFPE DNA extraction in terms of quantity of DNA obtained. All six extraction methods (blood and FFPE) performed well in terms of purity. Although there were variances in the quantity of DNA obtained, there were no significant differences in the efficiency of these methods in yielding amplifiable DNA extracts, as demonstrated by β-actin for whole blood specimens. In evaluation of FFPE DNA extraction methods, the Qiagen AllPrep® FFPE DNA/RNA Mini Kit was the best for applications requiring larger amplicons, but for smaller amplicons the Maxwell was most consistent.
MeSH term(s)	Automation ; DNA/blood ; Electrophoresis, Polyacrylamide Gel ; Formaldehyde ; Genetic Techniques/instrumentation ; Humans ; Paraffin Embedding ; Polymerase Chain Reaction
Chemical Substances	Formaldehyde (1HG84L3525) ; DNA (9007-49-2)
Language	English
Publishing date	2011-10-25
Publishing country	Germany
Document type	Evaluation Studies ; Journal Article
ZDB-ID	1418007-8
ISSN	1437-4331 ; 1434-6621 ; 1437-8523
ISSN (online)	1437-4331
ISSN	1434-6621 ; 1437-8523
DOI	10.1515/CCLM.2011.763
Database	MEDical Literature Analysis and Retrieval System OnLINE

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