This is a list of peer-reviewed publications from the various stages of my career.

They can be tracked using my ORCID:
orcid.org/0000-0002-3789-1842

Invited and conference presentations are listed on another page.

INVITED EDITORIAL

P Pandey; RJ Doerksen “New drugs from natural products around the world,” Pharmaceutical Sciences, 22, 215-216 (2016). Invited editorial. doi: 10.15171/PS.2016.34

EDITORIAL

JD Wren; RJ Doerksen; IT Toby; B Nanduri; R Homayouni; P Manda; S Thakkar “Proceedings of the 2018 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) conference,” BMC Bioinformatics 20 (Suppl 2), 95 (2019). doi: 10.1186/s12859-019-2618-7

JOURNAL ARTICLES (117)

(Citations numbers are listed for some of the articles that contribute to my h-index of 34, from among >7000 citations, according to Google Scholar)

M Mushtaq; S Naz; S Ashraf; RJ Doerksen; Z Ul-Haq “Exploring the viral protease inhibitor space driven by consensus scoring-based virtual screening,” In Silico Pharmacology (accepted 10/2023).

K Chaturvedi; CS Anthony; P Pandey; RJ Doerksen; M Godfrey “Influence of structural characteristics on the binding of synthetic cannabinoids from the JWH family to the CB1 receptor: A computational study,” Journal of Molecular Graphics and Modeling 126, 108620 (2023). doi: 10.1016/j.jmgm.2023.108620 PMID: 37722351

P Samanta; SK Mishra; VH Pomin; RJ Doerksen “Docking and molecular dynamics simulations clarify binding sites for interactions of novel marine sulfated glycans with SARS-CoV-2 spike glycoprotein,” Molecules 28, 6413 (2023). Special Issue on “New Insights into Biomolecular Structures and Interactions”. doi: 10.3390/molecules28176413 PMID: 37687244

T Berida; SR McKee; S Chatterjee; D Manning; W Li; P Pandey; SK Tripathi; Y Mreyoud; A Smirnov; RJ Doerksen; M Jackson; C Ducho; CL Stallings; S Roy “Discovery, synthesis, and optimization of 1,2,4-triazolyl pyridines targeting Mycobacterium tuberculosis,” ACS Infectious Diseases (8/24/2023). doi: 10.1021/acsinfecdis.3c00341 PMID: 37788674

P Samanta; RJ Doerksen “Identifying FmlH lectin-binding small molecules for the prevention of Escherichia coli-induced urinary tract infections using hybrid fragment-based design and molecular docking,” Computers in Biology and Medicine 163, 107072 (2023). (IF = 6.7) doi: 10.1016/j.compbiomed.2023.107072 PMID: 37329611

A Police; VK Shankar; P Pandey; S Rangappa; RJ Doerksen; SN Murthy “Novel topical anandamide formulation for alleviating peripheral neuropathic pain,” International Journal of Pharmaceutics 641, 123085 (2023). doi: 10.1016/j.ijpharm.2023.123085 PMID: 37245739 (IF = 6.51)

   

CVL Moreira; ALG Faria; DPB Silva; AS Filho; AW Keasling; JK Zjawiony; P Pandey; RJ Doerksen; HB Napolitano; FF Rocha; EA Costa; OJ Fajemiroye “Heteroaromatic salvinorin A analogue (P-3l) elicits antinociceptive and anxiolytic-like effects,” Fitoterapia 167, 105488 (2023). doi: 10.1016/j.fitote.2023.105488 PMID: 36990290 (IF = 3.2)

           

AK Maurya; P Sharma; P Samanta; AA Shami; SK Misra; F Zhang; R Thara; D Kumar; D Shi; RJ Linhardt; JS Sharp; RJ Doerksen; R Tandon; VH Pomin “Structural update, anti-SARS-CoV-2, and anticoagulant effects of the two sulfated galactans from Botryocladia occidentalis,” International Journal of Biological Macromolecules 238, 124168 (2023). doi: 10.1016/j.ijbiomac.2023.124168 PMID: 36963552 (IF = 8.0)

NS Akins; SF Mohammed; P Pandey; SJ Kim; F Mahdi; MIH Khan; E Moss; CJ Worth; MM Keane; AG Chittiboyina; RJ Doerksen; JJ Paris; HV Le “Alleviation of cocaine withdrawal and pertinent interactions between salvinorin-based antagonists and kappa opioid receptor,” ACS Chemical Neuroscience 14, 958-976 (2023). doi: 10.1021/acschemneuro.2c00806 PMID: 36795782 (IF = 5.8)

K Chaturvedi; I Hewamanna; P Pandey; W Khan; Y-H Wang; AG Chittiboyina; RJ Doerksen; M Godfrey “Identification of the putative binding site of a benzimidazole opioid (etazene) and its metabolites on µ-opioid receptor: A human liver microsomal assay and systematic computational study,” Molecules 28, 1601 (2023). doi: 10.3390/molecules28041601 PMID: 36838590

P Pandey; M Kumarihamy; K Chaturvedi; MA Ibrahim; JA Lambert; M Godfrey; RJ Doerksen; I Muhammad “In vitro and in silico studies of neolignans from Magnolia grandiflora L. seeds against human cannabinoids and opioid receptors,” Molecules 28, 1253 (2023). doi:  10.3390/molecules28031253 Special issue on “New Insights into Biomolecular Structures and Interactions.”

Y Liu; P Gao; X Liang; Y Zhang; X Yu; X Xue; L Kockaya; P Pandey; RJ Doerksen; X Wang; G Yao; W Chu; X Chen; S Song; MT Hamann; L Li “Prenylated flavonoids with significant anti-hepatoma activity from Daphne giraldii and effects on Fibroblast Growth Factor Receptor 1 (FGFR1),” European Journal of Medicinal Chemistry 247, 115006 (2023). doi: 10.1016/j.ejmech.2022.115006 PMID: 36549116

R Alkhodier; SK Mishra; RJ Doerksen; DA Colby “Comparison of conformational analyses of naturally occurring flavonoid-O-glycosides with unnatural flavonoid-CF2-glycosides using molecular modeling,” Journal of Chemical Information & Modeling 63, 375-386 (2023). doi: 10.1021/acs.jcim.2c01147 PMID: 36512328

SB Kim; M Farrag; SK Mishra; SK Misra; JS Sharp; RJ Doerksen; VH Pomin “Selective 2-desulfation of tetrasaccharide-repeating sulfated fucans during oligosaccharide production by mild acid hydrolysis,” Carbohydrate Polymers 301A, 120316 (2023). doi: 10.1016/j.carbpol.2022.120316 PMID: 36436858

OT Shofolawe-Bakare; JU de Mel; SK Mishra; MA Hossain; CM Hamadani; MC Pride; GS Dasanayake; WA Monroe; EW Roth; EEL Tanner; RJ Doerksen; AE Smith; TA Werfel “ROS-responsive glycopolymeric nanoparticles for enhanced drug delivery to macrophages,” Macromolecular Bioscience 22, 202200281 (2022). doi: 10.1002/mabi.202200281 PMID: 36125638

M Nagae; T Hirata; H Tateno; SK Mishra; N Manbe; N Osada; Y Tokoro; Y Yamaguchi; RJ Doerksen; T Shimizu; Y Kizuka “Discovery of a lectin domain that regulates enzyme activity in mouse N-acetylglucosaminyltransferase-IVa (MGAT4A),” Communications Biology 5, 695 (2022). doi: 10.1038/s42003-022-03661-w PMID: 35854001

NA Khaje; A Eletsky; SE Biehn; CK Mobley; MJ Rogals; Y Kim; SK Mishra; RJ Doerksen; S Lindert; JH Prestegard; JS Sharp “Validated determination of NRG1 Ig-like domain structure by mass spectrometry coupled with computational modeling,” Communications Biology 5, 452 (2022). doi: 10.1038/s42003-022-03411-y PMID: 35551273

SB Kim; M Zoepfl; P Samanta; F Zhang; K Xia; R Thara; RJ Linhardt; RJ Doerksen; MA McVoy; VH Pomin “Fractionation of sulfated galactan from the red alga Botryocladia occidentalis separates its anticoagulant and anti-SARS-CoV-2 properties,” Journal of Biological Chemistry 298, 101856 (2022). doi: 10.1016/j.jbc.2022.101856 PMID: 35337800

AM Vibhute; H-N Tanaka; SK Mishra; M Nagae; C Yonekawa; H Korekane; RJ Doerksen; H Ando; Y Kizuka “Structure-based design of UDP-GlcNAc analogs as candidate GnT-V inhibitors,” accepted to BBA General Subjects 1866(6): 130118 (3/4/2022). doi: 10.1016/j.bbagen.2022.130118 PMID: 35248671.

AH Tarawneh; P Pandey; LA Al-Momani; AV Gadetskaya; ST Abu-Orabie; RJ Doerksen; SJ Cutler “1,2,3-Triazole derivatives as highly selective cannabinoid receptor type 2 (CB2) agonists,” Arabian Journal of Chemistry 15, 103545 (2022). doi: 10.1016/j.arabjc.2021.103545

R Dwivedi; P Samanta; P Sharma; F Zhang; SK Mishra; P Kucheryavy; SB Kim; AO Aderibigbe; RJ Linhardt; R Tandon; RJ Doerksen; VH Pomin “Structural and kinetic analyses of holothurian sulfated glycans suggest potential treatment for SARS-CoV-2 infection,” Journal of Biological Chemistry 297, 101207 (2021). doi: 10.1016/j.jbc.2021.101207 PMID: 34537241

ND Chaurasiya; H Liu; RJ Doerksen; NPD Nanayakkara; LA Walker; BL Tekwani “Enantioselective interactions of anti-infective 8-aminoquinoline therapeutics with human monoamine oxidases A and B,” Pharmaceuticals 14, 398 (2021). doi: 10.3390/ph14050398

VK Shankar; A Police; P Pandey; ZG Cuny; MA Repka; RJ Doerksen; SN Murthy “Optimization of sulfobutyl-ether-β-cyclodextrin levels in oral formulations to enhance progesterone bioavailability,” International Journal of Pharmaceutics 596, 120212 (2021). doi: 10.1016/j.ijpharm.2021.120212

AO Aderibigbe; P Pandey; RJ Doerksen “Negative allosteric modulators of cannabinoid receptor 1: Modeling of ORG27569 interactions on CB1 bound to CP55940 in light of recent X-ray structures,” Journal of Biomolecular Structure and Dynamics (accepted: 1/4/2021; published online 1/22/2021). doi: 10.1080/07391102.2021.1873187

P Pandey; S Chatterjee; T Berida; RJ Doerksen; S Roy “Identification of potential non-nucleoside MraY inhibitors for tuberculosis chemotherapy using structure-based virtual screening,” Journal of Biomolecular Structure and Dynamics (accepted: 12/7/2020; published online 12/22/2020). doi: 10.1186/s12859-019-2618-7

ND Chaurasiya; J Midiwo; P Pandey; RN Bwire; RJ Doerksen; I Muhammad; BL Tekwani “Selective interactions of O-methylated flavonoid natural products with human monoamine oxidase-A and -B,” Molecules 25, 5358 (2020). Special issue in honor of Prof. James D. McChesney on the occasion of his 80th birthday. doi: 10.3390/molecules25225358

P Pandey; B Avula; IA Khan; SI Khan; VJ Navarro; RJ Doerksen; AG Chittiboyina “Potential modulation by EGCG and its metabolites of human NAD[P]H-quinone oxidoreductase 1 (NQO1) – A systematic computational study,” Chemical Research in Toxicology 33, 2749-2764 (2020). doi: 10.1021/acs.chemrestox.9b00450

MNG Amin; J Kusnadi; J-L Hsu; RJ Doerksen; T-C Huang “Identification of a novel umami peptide in tempeh (Indonesian fermented soybean) and its binding mechanism to the umami receptor T1R,” Food Chemistry 333, 127411 (2020). doi: 10.1016/j.foodchem.2020.127411

AL Duddupudi; P Pandey; H Vo; CL Welsh; RJ Doerksen; GD Cuny “Hypervalent iodine mediated oxidative cyclization of acrylamide N-carbamates to 5,5-disubstituted oxazolidine-2,4-diones,” Journal of Organic Chemistry 85, 7549-7557 (2020). doi: 10.1021/acs.joc.0c00581 PMID:

YP Singh; GN Venkata; C Tej; A Pandey; K Priya; P Pandey; G Shankar; PK Nayak; G Rai; AG Chittiboyina; RJ Doerksen; S Vishwakarma; G Modi “Design, synthesis and biological evaluation of novel naturally-inspired multifunctional molecules for the management of Alzheimer’s Disease,” European Journal of Medicinal Chemistry 198, 112257 (2020). doi: 10.1016/j.ejmech.2020.112257 PMID:

 

SK Tripathi; Q Feng; L Liu; DE Levin; KK Roy; RJ Doerksen; SR Baerson; X Shi; X Pan; W-H Xu; X-C Li; AM Clark; AK Agarwal “Puupehenone, a marine sponge-derived sesquiterpene quinone, potentiates the antifungal drug caspofungin by disrupting Hsp90 activity and the cell wall integrity pathway,” mSphere 5, e00818-19 (2020). doi: 10.1128/mSphere.00818-19 PMID: 31915228

FF Bezerra; WP Vignovich; AO Aderibigbe; H Liu; J Sharp; RJ Doerksen; VH Pomin “Conformational properties of L-fucose and the tetrasaccharide building block of the sulfated L-fucan from Lytechinus variegatus,” Journal of Structural Biology 209, 107407 (2020). doi: 10.1016/j.jsb.2019.107407 PMID: 31698075

 

P Pandey; KK Roy; RJ Doerksen “Negative allosteric modulators of cannabinoid receptor 2: Protein modeling, binding site identification and molecular dynamics simulations in the presence of an orthosteric agonist,” Journal of Biomolecular Structure and Dynamics 38, 32-47 (2020). doi: 10.1080/07391102.2019.1567384 PMID: 30652534

J Liu; P Pandey; X Wang; K Adams; X Qi; J Chen; H Sun; Q Hou; D Ferreira; RJ Doerksen; S Li; MT Hamann “Hepatoprotective tetrahydrobenzocyclooctabenzofuranone lignans from Kadsura longipedunculata,” Journal of Natural Products 82, 2842-2851 (2019). https://doi.org/10.1021/acs.jnatprod.9b00576 PMID: 31556297

  

AW Keasling; P Pandey; RJ Doerksen; GR Pedrino; EA Costa; LC da Cunha; JK Zjawiony; JO Fajemiroye “Salvindolin elicits opioid system-mediated antinociceptive and antidepressant-like activities,” Journal of Psychopharmacology 33, 865-881 (2019). doi: 10.1177/0269881119849821 PMID: 31192780

Y Zou; X Wang; J Sims; B Wang; P Pandey; CL Welsh; RP Stone; MA Avery; RJ Doerksen; D Ferreira; C Anklin; FA Valeriote; M Kelly; MT Hamann “Computationally-assisted discovery and assignment of a highly strained and PANC-1 selective alkaloid from Alaska’s deep ocean,” Journal of the American Chemical Society 141, 4338-4344 (2019). doi: 10.1021/jacs.8b11403 PMID: 30758203

ND Chaurasiya; J Zhao; P Pandey; RJ Doerksen; I Muhammad; BL Tekwani “Selective inhibition of human monoamine oxidase B by acacetin 7-methyl ether isolated from Turnera diffusa (damiana),” Molecules 24, 810 (2019). doi: 10.3390/molecules24040810 PMID: 30813423 Special memorial issue honoring Dr. Charles F. Hufford.

P Pandey; KK Roy; H Liu; G Ma; SA Pettaway; WF Alsharif; RS Gadepalli; JM Rimoldi; CR McCurdy; SJ Cutler; RJ Doerksen “Structure-based identification of potent natural product chemotypes as cannabinoid receptor 1 inverse agonists,” Molecules 23, 2630 (2018). Invited. Special issue on “Hit Generation and Verification for Novel Lead Compounds”. doi: 10.3390/molecules23102630 PMID: 30322136

LG Malak; MA Ibrahim; AM Moharram; P Pandey; B Tekwani; RJ Doerksen; D Ferreira; SA Ross “Antileishmanial Carbasugars from Geosmithia langdonii,” Journal of Natural Products 81, 2222-2227 (2018). doi: 10.1021/acs.jnatprod.8b00473 PMID: 30298736

X Wang; J Liu; P Pandey; FR Fronczek; RJ Doerksen; J Chen; X Qi; P Zhang; D Ferreira; FA Valeriote; H Sun; S Li; MT Hamann “Computationally assisted assignment of the kadsuraols, a class of chemopreventive agents for the control of liver cancer,” Organic Letters 20, 5559-5563 (2018). doi: 10.1021/acs.orglett.8b02207 PMID: 30192555

P Pandey; ND Chaurasiya; BL Tekwani; RJ Doerksen “Interactions of endocannabinoid virodhamine and related eicosanoids with human monoamine oxidase-A and -B,” Biochemical Pharmacology 155, 82-91 (2018). doi: 10.1016/j.bcp.2018.06.024 PMID: 29958841

MF Sowaileh; AE Salyer; KK Roy; JP John; JR Woods; RJ Doerksen; GH Hockerman; DA Colby “Agonists of the γ-aminobutyric acid type B (GABA_B) receptor derived from b-hydroxy and b-amino difluoromethyl ketones,” Bioorganic and Medicinal Chemistry Letters 28, 2697-2700 (2018). doi: 10.1016/j.bmcl.2018.04.003 PMID: 29657102

J Liu; P Pandey; X Wang; X Qi; J Chen; H Sun; P Zhang; Y Ding; D Ferreira; RJ Doerksen; MT Hamann; S Li “Hepatoprotective dibenzocyclooctadiene and tetrahydrobenzocyclooctabenzofuranone lignans from Kadsura longipedunculata,” Journal of Natural Products 81, 846-857 (2018). doi: 10.1021/acs.jnatprod.7b00934 PMID: 29595972

GC Brandão; FCR Missias; LM Arantes; LF Soares; KK Roy; RJ Doerksen; A Braga de Oliveira; GR Pereira “Antimalarial naphthoquinones. Synthesis via click chemistry, in vitro activity, docking to PfDHODH and SAR of lapachol-based compounds,” European Journal of Medicinal Chemistry, 145, 191-205 (2018). doi: 10.1016/j.ejmech.2017.12.051 PMID: 29324340

J Pressly; SM Mustafe; A Sahar; P Pandey; KK Roy; RJ Doerksen; BM Moore; F Park “Selective cannabinoid 2 receptor stimulation reduces tubular epithelial cell damage following renal ischemia-reperfusion injury,” Journal of Pharmacology and Experimental Therapeutics, 364, 287-299 (2018). doi: 10.1124/jpet.117.245522 PMID: 29187590 PMCID: PMC5774215.

X Wang; J Liu; P Pandey; J Chen; FR Fronczek; S Parnham; X Qi; RJ Doerksen; D Ferreira; H Sun; S Li; MT Hamann “Assignment of the absolute configuration of hepatoprotective highly oxygenated triterpenoids using X-ray, ECD, NMR J-based configurational analysis and HSQC overlay experiments,” BBA (Biochimica et Biophysica Acta) General Subjects, 1861, 3089-3095 (2017). doi: 10.1016/j.bbagen.2017.09.001 PMID: 28919469

 

J Oh; H Liu; HB Park; D Ferreira; G-S Jeong; MT Hamann; RJ Doerksen; MK Na “In silico investigation of lavandulyl flavonoids for the 2 development of potent FAS-inhibitory prototypes,” BBA (Biochimica et Biophysica Acta) General Subjects, 1861, 3180-3188 (2017). doi: 10.1016/j.bbagen.2016.08.001 PMID: 27531709

 

Y Ding; H Liu; BL Tekwani; NPD Nanayakkara; IA Khan; LA Walker; RJ Doerksen “Methemoglobinemia hemotoxicity of some antimalarial 8-aminoquinoline analogues and their hydroxylated derivatives: Density functional theory computation of ionization potentials,” Chemical Research in Toxicology, 29, 1132-1141 (2016). doi: 10.1021/acs.chemrestox.6b00063 PMID: 27223244

NN Mohammed; P Pandey; KM Elokely; HL Liu; RJ Doerksen; MA Repka “Clotrimazole-cyclodextrin based approach for the management and treatment of Candidiasis. A formulation and chemistry based evaluation,” Pharmaceutical Development and Technology, 21, 619-629 (2016). doi: 10.3109/10837450.2015.1041041 PMID: 25923135

AD Priyanto; RJ Doerksen; C-I Chang; Y-C Lin; T-C Wang; SB Widjanarko; J Kusnadi; J-L Hsu “Screening, discovery, and characterization of angiotensin-I converting enzyme inhibitory peptides derived from proteolytic hydrolysate of bitter melon seed proteins,” Journal of Proteomics, 128, 424-435 (2015). doi: 10.1016/j.jprot.2015.08.018 PMID: 26344130

              

AD Priyanto; RJ Doerksen; C-I Chang; Y-C Lin; T-C Wang; SB Widjanarko; J Kusnadi; J-L Hsu “Data in support of optimized production of angiotensin-I converting enzyme inhibitory peptides derived from proteolytic hydrolysate of bitter melon seed proteins,” Data in Brief, 5, 403-407 (2015). doi: 10.1016/j.dib.2015.09.038 PMID: 26958600

J Bae; LE McNamara; MA Nael; RJ Doerksen; GL Bidwell III; NI Hammer; S Jo “Nitroreductase specific activatable fluorescent probe for imaging,” Chemical Communications, 51, 12787-12790 (2015). doi: 10.1039/C5CC03824C Cited 55 times.

     

KM Brown; KK Roy; GH Hockerman; RJ Doerksen; DA Colby “Activation of the γ-aminobutyric acid type B (GABA_B) receptor by agonists and positive allosteric modulators.“ Journal of Medicinal Chemistry, 58, 6336-6347 (2015). (Miniperspective) doi: 10.1021/jm5018913 Cited 36 times.

CC Chen; M-L Wu; C-T Ho; RJ Doerksen; T-C Huang “Apoptotic induction by andrographolide in HL-60 cells via Ras/ERK/NF-κB and Ras/Akt/NF-κB signaling dependent down-regulation of glyoxalase 1 and HMG-CoA reductase.” Journal of Functional Foods, 14, 226-235 (2015). doi: 10.1016/j.jff.2015.01.048

P-S Su; RJ Doerksen; S-H Chen; W-C Sung; RDS Rawendra; C-R Chen; J-W Li; Aisha; T-C Huang; C-I Chang; M-H Liao; J-L Hsu “Screening and profiling stilbene-type natural products with angiotensin-converting enzyme inhibitory activity from Ampelopsis brevipedunculata var. hancei (Planch.) Rehder,” Journal of Pharmaceutical and Biomedical Analysis, 108, 70-77 (2015). doi: 10.1016/j.jpba.2015.01.053 Cited 32 times.

  

H Liu; Y Ding; LA Walker; RJ Doerksen “Computational study on the effect of exocyclic substituents on the ionization potential of primaquine: Insights into the design of primaquine-based antimalarial drugs with less methemoglobin generation,” Chemical Research in Toxicology, 28, 169-174 (2015). doi: 10.1021/tx500230t PMID: 25222923

A Chatterjee; SJ Cutler; RJ Doerksen; IA Khan; JS Williamson “Discovery of novel thienoquinolone derivatives as selective and ATP non-competitive CDK5/p25 inhibitors by structure-based virtual screening,” Bioorganic & Medicinal Chemistry, 22, 6409-6421 (2014). doi: 10.1016/j.bmc.2014.09.043

                      

G Fu; P. Sivaprakasam; OR Dale; SP Manly; SJ Cutler; RJ Doerksen “Pharmacophore modeling, Ensemble docking, virtual screening, and biological evaluation on glycogen synthase kinase-3β.” Molecular Informatics, 33, 610–626 (2014). doi: 10.1002/minf.201400044

G Fu; S Liu; X Nan; OR Dale; Z Zhao; Y Chen; DE Wilkins; SP Manly; SJ Cutler; RJ Doerksen “Quantitative structure-activity relationship analysis and a combined ligand-based/structure-based virtual screening study for glycogen synthase kinase-3.” Molecular Informatics, 33, 627–640 (2014). doi: 10.1002/minf.201400045

Y Ding; H Liu; NPD Nanayakkara; IA Khan; BL Tekwani; LA Walker; RJ Doerksen “Hydroxylated derivatives of NPC1161: Theoretical insights into their potential toxicity and the feasibility and regioselectivity of their formation,” Journal of Physical Chemistry A, 118, 5501–5507 (2014). doi: 10.1021/jp502612t

H Liu; RY Patel; RJ Doerksen “Structure of the cannabinoid receptor 1: Homology modeling of the inactive state and enrichment study based on CB1 antagonist docking.” MedChemComm, 5, 1297-1302 (2014). doi: 10.1039/C4MD00121D Inside cover article.

  

MM Ghoneim; KM Elokely; AA El-Hela; AEI Mohammad; M Jacob; M Radwan; RJ Doeksen; SJ Cutler; SA Ross “Asphodosides A-E, anti-MRSA metabolites from Asphodelus microcarpus,” Phytochemistry, 105, 79-84 (2014). doi: 10.1016/j.phytochem.2014.06.011

         

MM Ghoneim, KM Elokely; AA El-Hela; AEI Mohammad; M Jacob; SJ Cutler; RJ Doerksen; SA Ross “Isolation and characterization of new secondary metabolites from Asphodelus microcarpus,” Medicinal Chemistry Research, 23, 3510-3515 (2014). doi: 10.1007/s00044-014-0928-x

J Bae; MA Nael; L Jiang; PT Hwang; F Mahdi; H-W Jun; WM Elshamy; Y-D Zhou; SN Murthy; RJ Doerksen; S Jo “Quinone propionic acid-based redox-triggered polymer nanoparticles for drug delivery: Computational analysis and in vitro evaluation,” Journal of Applied Polymer Science, 131 (2014). doi: 10.1002/app.40461

H Liu; BL Tekwani; NPD Nanayakkara; LA Walker; RJ Doerksen “Methemoglobin generation by 8-aminoquinolines: Effect of substitution at 5-position of primaquine,” Chemical Research in Toxicology, 26, 1801-1809 (2013). doi: 10.1021/tx400067a

 

MAM Ibrahim; M Na; J Oh; RF Schinazi; TR McBrayer; T Whitaker; RJ Doerksen; DJ Newman; LG Zachos; MT Hamann “Significance of endangered and threatened plant natural products in the control of human disease,” Proceedings of the National Academy of Sciences of the United States of America, 110, 16832-16837 (2013). doi: 10.1073/pnas.1311528110 Featured article in University of Washington’s Conservation Magazine and “Featured article recommended for teaching” in “F1000Prime”. Cited 41 times.

Z Zhao; G Fu; S Liu; KM Elokely; RJ Doerksen; Y Chen; DE Wilkins “Drug activity prediction using multiple-instance learning via joint instance and feature selection,” BMC Bioinformatics, 14 (Suppl 14), S16 (12 pp) (2013). (2013 MCBIOS Proceedings). doi: 10.1186/1471-2105-14-S14-S16

IH Hwang; J Oh; A Kochanowska-Karamyan; RJ Doerksen; M Na; MT Hamann “A novel natural phenyl alkene with cytotoxic activity,” Tetrahedron Letters, 54, 3872-3876 (2013). doi: 10.1016/j.tetlet.2013.05.032

H Liu; Y Ding; LA Walker; RJ Doerksen “Effect of antimalarial drug primaquine and its derivatives on the ionization potential of hemoglobin: A QM/MM study,” MedChemComm, 4, 1145-1147 (2013). doi: 10.1039/C3MD00045A Cover article, August 2013.

KM Elokely; RJ Doerksen “Docking challenge: Protein sampling and molecular docking performance,” Journal of Chemical Information & Modeling, 53, 1934–1945 (2013). doi: 10.1021/ci400040d PMID: 23530568 Featured on the cover of Issue 11, November 2013. Cited >106 times.

J Oh; JJ Bowling; Y Zou; AG Chittiboyina; RJ Doerksen; D Ferreira; TD Leininger; MT Hamann “Configurational assignments of conformationally restricted bis-monoterpene hydroquinones: Utility in exploration of endangered plants,” Biochemica et Biophysica Acta (BBA) – General Subjects, 1830, 4229-4234 (2013). doi: 10.1016/j.bbagen.2013.04.029; PMID: 23628705

MA Albadry; KM Elokely; B Wang; JJ Bowling; MF Abdelwahab; MH Hossein; RJ Doerksen; MT Hamann “Computationally assisted assignment of Kahalalide Y configuration using an NMR-constrained conformational search,” Journal of Natural Products, 76, 178-185 (2013). doi: 10.1021/np3006088; PMID: 23363083

A Shayanfar; S Ghasemi; S Soltani; K Asadpour-Zeynali; RJ Doerksen; A Jouyban “Quantitative structure-activity relationships of imidazole-containing farnesyltransferase inhibitors using different chemometric methods,” Medicinal Chemistry, 9, 434-448 (2013). doi: 10.2174/1573406411309030014

G Fu; X Nan; H Liu; RY Patel; PR Daga; Y Chen; DE Wilkins; RJ Doerksen “Implementation of multiple-instance learning in drug activity prediction,” BMC Bioinformatics, 13, (Suppl 15) S3 (2012). doi: 10.1186/1471-2105-13-S15-S3; PMID: 23046442 (2012 MCBIOS Proceedings).

G Fu; H Liu; RJ Doerksen “Molecular modeling to provide insight into the substrate binding and catalytic mechanism of human biliverdin-IXα reductase,” Journal of Physical Chemistry B, 116, 9580-9594 (2012). doi: 10.1021/jp301456j; PMID: 22823425

S Liu; RY Patel; PR Daga; H Liu; G Fu; RJ Doerksen; Y Chen; D Wilkins “Combined rule extraction and feature elimination in supervised classification,” IEEE Transactions on Nanobioscience, 11, 228-236 (2012). doi: 10.1109/TNB.2012.2213264; PMID: 22987128

LK Brents; F Medina-Bolivar; KA Seely; V Nair; SM Bratton; A Gallus-Zawada; L Ñopo; RY Patel; H Liu; RJ Doerksen; PL Prather; A Radominska-Pandya “Natural prenylated resveratrol analogs arachidin-1 and -3 demonstrate improved glucuronidation profiles and have affinity for cannabinoid receptors,” Xenobiotica, 42, 139-156 (2012). doi: 10.3109/00498254.2011.609570

H Liu; LA Walker; RJ Doerksen “DFT study on the radical anions formed by primaquine and its derivatives,” Chemical Research in Toxicology, 24, 1476-1485 (2011). doi: 10.1021/tx200094v; PMID: 21699254

H Liu; A Dasmahapatra; RJ Doerksen “Computational study on the conformations of gambogic acid,” Chemical Physics Letters, 511, 405-412 (2011). doi: 10.1016/j.cplett.2011.06.035; PMID: 22991483

 

X Nan; G Fu; Z Zhao; S Liu; RY Patel; H Liu; PR Daga; RJ Doerksen; X Dang; Y Chen; D Wilkins “Leveraging domain information to restructure biological prediction.” BMC Bioinformatics, 12, S22 (15 pp.) (2011) (2011 MCBIOS Proceedings). doi: 10.1186/1471-2105-12-S10-S22; PMID: 22166097

H Liu; LA Walker; NPD Nanayakkara; RJ Doerksen “Methemoglobinemia caused by 8-aminoquinoline drugs: DFT calculations suggest an analogy to H₄B’s role in nitric oxide synthase,” Journal of the American Chemical Society, 133, 1172-1175 (2011). doi: 10.1021/ja107472c; PMID: 21244096

G Fu; RJ Doerksen; P Xu “Ab initio calculations of optical rotations and ¹H chemical shifts allow absolute configuration assignment of sulfinyl dilactones,” Journal of Molecular Structure, 987, 166-173 (2011). doi: 10.1016/j.molstruc.2010.11.076

RY Patel; RJ Doerksen “Protein kinases-inhibitor database: analysis of structure variability and protein-inhibitor interactions within the P-loop,” Journal of Proteome Research, 9, 4433-4442 (2010). doi: 10.1021/pr100662s; PMID: 20681595 Cited 42 times.

FE Dayan; PR Daga; SO Duke; RM Lee; PJ Tranel; RJ Doerksen “Biochemical and structural consequences of a glycine deletion in the α-8 helix of protoporphyrinogen oxidase,” BBA – Proteins and Proteomics, 1804, 1548-1556 (2010). doi: 10.1016/j.bbapap.2010.04.004 Cited 51 times.

R Mohammed; J Peng; M Kelly; M Yousaf; E Winn; S Odde; Z Bie; A Xie; RJ Doerksen; MT Hamann “Polyketide-peroxides from a species of Jamaican plakortis (Porifera: Demospongiae),” Australian Journal of Chemistry, 63, 1-9 (2010). Special Issue. doi: 10.1071/CH09665

        

PR Daga; J Duan; RJ Doerksen “Understanding protein-ligand interactions in hepatitis B virus DNA polymerase by homology modeling, molecular docking, and molecular dynamics simulations,” Protein Science, 19, 796-807 (2010). doi: 10.1002/pro.359; PMID: 20162615

H Liu; CR McCurdy; RJ Doerksen “Computational study on the conformations of mitragynine and mitragynaline,” Journal of Molecular Structure: Theochem, 945, 57-63 (2010). doi: 10.1016/j.theochem.2010.01.011; PMID: 21293786

J Peng; S Kudrimoti; S Prasanna; S Odde; RJ Doerksen; HK Pennaka; Y-M Choo; KV Rao; BL Tekwani; V Madgula; SI Khan; B Wang; AMS Mayer; MR Jacob; LC Tu; J Gertsch; MT Hamann “Structure activity relationship and mechanism of action studies of manzamine analogues for the control of neuroinflammation and cerebral infections,” Journal of Medicinal Chemistry, 53, 61-76 (2010). doi: 10.1021/jm900672t; PMID: 20017491 Cited 72 times.

PR Daga; RY Patel; RJ Doerksen “Template-based protein modeling: Recent methodological advances,” Current Topics in Medicinal Chemistry, 10, 84-94 (2010). PRD and RYP were joint first authors. (Invited review.) doi: 10.2174/156802610790232314 PMID: 19929829 Cited 49 times.

S Kudrimoti; SA Ahmed; PR Daga; AE Wahba; SI Khalifa; RJ Doerksen; MT Hamann “Semisynthetic latrunculin B analogs: Studies of actin docking support a proposed mechanism for latrunculin bioactivity,” Bioorganic & Medicinal Chemistry, 17, 7517-7522 (2009). doi: 10.1016/j.bmc.2009.09.012; PMID: 19800245

P Sivaprakasam; PN Tosso; RJ Doerksen “Structure-activity relationship and comparative docking studies for cycloguanil analogs as PfDHFR-TS inhibitors,” Journal of Chemical Information & Modeling, 49, 1787-1796 (2009). doi: 10.1021/ci9000663; PMID: 19588935

A Xie; S Odde; P Sivaprakasam; RJ Doerksen “Imidazole-containing farnesyltransferase inhibitors: 3D quantitative structure-activity relationship and molecular docking studies,” Journal of Computer-Aided Molecular Design, 23, 431-448 (2009). doi: 10.1007/s10822-009-9278-z; PMID: 19479325

A Xie; SR Clark; S Prasanna; RJ Doerksen “3D quantitative structure-farnesyltransferase inhibition analysis for some diaminobenzophenones,” Journal of Enzyme Inhibition & Medicinal Chemistry, 24, 1220-1228 (2009). doi: 10.3109/14756360902781389; PMID: 19912055

S Prasanna; RJ Doerksen “Topological polar surface area: A useful descriptor in 2D-QSAR,” Current Medicinal Chemistry, 16, 21-41 (2009). doi: 10.2174/092986709787002817 PMID: 19149561 Cited 86 times.

S Prasanna; PR Daga; A Xie; RJ Doerksen “Glycogen synthase kinase-3 inhibition by 3-anilino-4-phenylmaleimides: Insights from 3D-QSAR and docking,” Journal of Computer-Aided Molecular Design, 23, 113-127 (2009). doi: 10.1007/s10822-008-9244-1 PMID: 18839067

MA Ibrahim; AG Shilabin; S Prasanna; M Jacob; SI Khan; RJ Doerksen; MT Hamann “2-N-Methyl modifications and SAR studies of manzamine A,” Bioorganic & Medicinal Chemistry, 16, 6702-6706 (2008). PMID: 18595720 Cited 30 times.

PR Daga; RJ Doerksen “Stereoelectronic properties of spiroquinazolinones in differential PDE7 inhibitory activity,” Journal of Computational Chemistry 29, 1945-1954 (2008). doi: 10.1002/jcc.20960 PMID: 18366018

SA Ahmed; S Odde; PR Daga; JJ Bowling; MK Mesbah; DT Youssef; SI Khalifa; RJ Doerksen; MT Hamann “Latrunculin with a highly oxidized thiazolidinone ring:  Structure assignment and actin docking,” Organic Letters 9, 4773-4776 (2007). doi: 10.1021/ol7020675 Cited 31 times.

P Sivaprakasam; A Xie; RJ Doerksen “Probing the physicochemical and structural requirements for glycogen synthase kinase-3α inhibition: 2D-QSAR for 3-anilino-4-phenylmaleimides,” Bioorganic & Medicinal Chemistry 14, 8210-8218 (2006). doi: 10.1016/j.bmc.2006.09.021; PMID: 17010615 Cited 52 times.

A Xie; P Sivaprakasam; RJ Doerksen “3D-QSAR analysis of antimalarial farnesyltransferase inhibitors based on a 2, 5-diaminobenzophenone scaffold,” Bioorganic & Medicinal Chemistry 14, 7311-7323 (2006). doi: 10.1016/j.bmc.2006.06.041; PMID: 16837204 Cited 42 times.

Y Shao; LF Molnar; Y Jung; J Kussmann; C Ochsenfeld; ST Brown; ATB Gilbert; LV Slipchenko; SV Levchenko; DP O’Neill; RA DiStasio; RC Lochan; T Wang; GJO Beran; NA Besley; JM Herbert; CY Lin; T Van Voorhis; SH Chien; A Sodt; RP Steele; VA Rassolov; PE Maslen; PP Korambath; RD Adamson; B Austin; J Baker; EFC Byrd; H Dachsel; RJ Doerksen; A Dreuw; BD Dunietz; AD Dutoi; TR Furlani; SR Gwaltney; A Heyden; S Hirata; CP Hsu; G Kedziora; RZ Khalliulin; P Klunzinger; AM Lee; MS Lee; W Liang; I Lotan; N Nair; B Peters; EI Proynov; PA Pieniazek; YM Rhee; J Ritchie; E Rosta; CD Sherrill; AC Simmonett; JE Subotnik; HL Woodcock; W Zhang; AT Bell; AK Chakraborty; DM Chipman; FJ Keil; A Warshel; WJ Hehre; HF Schaefer; J Kong; AI Krylov; PMW Gill; M Head-Gordon “Advances in methods and algorithms in a modern quantum chemistry program package,” Physical Chemistry Chemical Physics 8, 3172-3191 (2006). doi: 10.1039/B517914A Cited >2576 times. Invited article.

H Tang; RJ Doerksen; TV Jones; ML Klein; GN Tew “Biomimetic facially amphiphilic antibacterial oligomers with conformationally stiff backbones,” Chemistry & Biology 13, 427-435 (2006). doi: 10.1016/j.chembiol.2006.02.007 Cited 84 times.

H Tang; RJ Doerksen; GN Tew “Synthesis of urea oligomers and their antibacterial activity,” Chemical Communications, 1537-1539 (2005). doi: 10.1039/B413679A Cited 71 times.

RJ Doerksen; B Chen; D Liu; GN Tew; WF DeGrado; ML Klein “Controlling the conformation of arylamides: Computational studies of intramolecular hydrogen bonds between amides and ethers or thioethers,” Chemistry: A European Journal 10, 5008 (2004). doi: 10.1002/chem.200400176 Cited 37 times.

D Liu; S Choi; B Chen; RJ Doerksen; DJ Clements; JD Winkler; ML Klein; WF DeGrado “Nontoxic membrane-active antimicrobial arylamide oligomers,” Angewandte Chemie International Edition 44, 1158 (2004). doi: 10.1002/anie.200352791″ Cited 235 times. Cover article, February 20, 2004.

RJ Doerksen; VJ Steeves; AJ Thakkar “Are polarizabilities useful as aromaticity indices? Tests on azines, azoles, oxazoles and thiazoles,” Special issue on polarizabilities. Journal of Computational Methods in Science and Engineering 3, 427-438 (2004). Also appears in Computational Aspects of Electric Polarizability Calculations: Atoms, Molecules and Clusters, G Maroulis (Editor) IOS Press, Amsterdam (2004). ISBN: 158603495

RJ Doerksen; B Chen; J Yuan; JD Winkler; ML Klein “Novel conformationally-constrained β-peptides characterized by ¹H NMR chemical shifts,” Chemical Communications, 2534 (2003). doi: 10.1039/B309584C Cited 29 times.

RJ Doerksen; B Chen; ML Klein “Intramolecular hydrogen bonds: Ab initio Car-Parrinello simulations of arylamide torsions,” Chemical Physics Letters 380, 150 (2003). doi: 10.1016/j.cplett.2003.08.112

GN Tew; D Liu; B Chen; RJ Doerksen; J Kaplan; PJ Carroll; ML Klein; WF DeGrado “De novo design of biomimetic antimicrobial polymers,” Proceedings of the National Academy of Sciences of the United States of America 99, 5110 (2002). Featured in Chemical & Engineering News 80, No. 23, 36-38 (June 10, 2002). Also, featured in the year-end Chemistry Highlights 2002 of Chemical & Engineering News 80, No. 50, 47 (December 16, 2002). doi: 10.1073/pnas.082046199 Cited 484 times.

RJ Doerksen; AJ Thakkar “Bond orders in heteroaromatic rings,” International Journal of Quantum Chemistry 90, 534 (2002). doi: 10.1002/qua.998

RJ Doerksen; AJ Thakkar “Quadrupole and octopole moments of heteroaromatic rings,” Journal of Physical Chemistry A 103, 10009 (1999). doi: 10.1021/jp992524v Cited 66 times.

RJ Doerksen; AJ Thakkar “Structures, vibrational frequencies and polarizabilities of diazaborinines, triazadiborinines, azaboroles, and oxazaboroles,” Journal of Physical Chemistry A 103, 2141 (1999). doi: 10.1021/jp984256r Cited 39 times.

RJ Doerksen; AJ Thakkar; T Koga; M Hayashi “Geometries and multipole moments of AlH₄^–, SiH₄, PH₃, H₂S and HCl,” Theochem 488, 217 (1999). doi: 10.1016/S0166-1280(99)00020-2

RJ Doerksen; AJ Thakkar “Azaborinines: Structures, vibrational frequencies and polarizabilities,” Journal of Physical Chemistry A 102, 4679 (1998). doi: 10.1021/jp980778v

RJ Doerksen; AJ Thakkar “Polarizabilities of heteroaromatic molecules: Azines revisited,” International Journal of Quantum Chemistry 60, 421 (1996). doi: ijqc.html#60(1):October:1996 Cited 27 times.

N El-Bakali Kassimi; RJ Doerksen; AJ Thakkar “Polarizabilities of oxazoles: ab initio calculations and simple models,” Journal of Physical Chemistry 100, 8752 (1996). doi: 10.1021/jp953425u Cited 37 times.

N El-Bakali Kassimi; RJ Doerksen; AJ Thakkar “Polarizabilities of aromatic five-membered rings: Azoles,” Journal of Physical Chemistry 99, 12790 (1995). doi: 10.1021/j100034a01 Cited 58 times.