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Chittum JE, Thompson A, Desai UR. Glycosaminoglycan microarrays for studying glycosaminoglycan-protein systems. Carbohydr Polym 2024; 335:122106. [PMID: 38616080 PMCID: PMC11032185 DOI: 10.1016/j.carbpol.2024.122106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/16/2024]
Abstract
More than 3000 proteins are now known to bind to glycosaminoglycans (GAGs). Yet, GAG-protein systems are rather poorly understood in terms of selectivity of recognition, molecular mechanism of action, and translational promise. High-throughput screening (HTS) technologies are critically needed for studying GAG biology and developing GAG-based therapeutics. Microarrays, developed within the past two decades, have now improved to the point of being the preferred tool in the HTS of biomolecules. GAG microarrays, in which GAG sequences are immobilized on slides, while similar to other microarrays, have their own sets of challenges and considerations. GAG microarrays are rapidly becoming the first choice in studying GAG-protein systems. Here, we review different modalities and applications of GAG microarrays presented to date. We discuss advantages and disadvantages of this technology, explain covalent and non-covalent immobilization strategies using different chemically reactive groups, and present various assay formats for qualitative and quantitative interpretations, including selectivity screening, binding affinity studies, competitive binding studies etc. We also highlight recent advances in implementing this technology, cataloging of data, and project its future promise. Overall, the technology of GAG microarray exhibits enormous potential of evolving into more than a mere screening tool for studying GAG - protein systems.
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Affiliation(s)
- John E Chittum
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, United States of America; Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, United States of America
| | - Ally Thompson
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, United States of America; Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, United States of America
| | - Umesh R Desai
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, United States of America; Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, United States of America.
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Wallach I, Bernard D, Nguyen K, Ho G, Morrison A, Stecula A, Rosnik A, O’Sullivan AM, Davtyan A, Samudio B, Thomas B, Worley B, Butler B, Laggner C, Thayer D, Moharreri E, Friedland G, Truong H, van den Bedem H, Ng HL, Stafford K, Sarangapani K, Giesler K, Ngo L, Mysinger M, Ahmed M, Anthis NJ, Henriksen N, Gniewek P, Eckert S, de Oliveira S, Suterwala S, PrasadPrasad SVK, Shek S, Contreras S, Hare S, Palazzo T, O’Brien TE, Van Grack T, Williams T, Chern TR, Kenyon V, Lee AH, Cann AB, Bergman B, Anderson BM, Cox BD, Warrington JM, Sorenson JM, Goldenberg JM, Young MA, DeHaan N, Pemberton RP, Schroedl S, Abramyan TM, Gupta T, Mysore V, Presser AG, Ferrando AA, Andricopulo AD, Ghosh A, Ayachi AG, Mushtaq A, Shaqra AM, Toh AKL, Smrcka AV, Ciccia A, de Oliveira AS, Sverzhinsky A, de Sousa AM, Agoulnik AI, Kushnir A, Freiberg AN, Statsyuk AV, Gingras AR, Degterev A, Tomilov A, Vrielink A, Garaeva AA, Bryant-Friedrich A, Caflisch A, Patel AK, Rangarajan AV, Matheeussen A, Battistoni A, Caporali A, Chini A, Ilari A, Mattevi A, Foote AT, Trabocchi A, Stahl A, Herr AB, Berti A, Freywald A, Reidenbach AG, Lam A, Cuddihy AR, White A, Taglialatela A, Ojha AK, Cathcart AM, Motyl AAL, Borowska A, D’Antuono A, Hirsch AKH, Porcelli AM, Minakova A, Montanaro A, Müller A, Fiorillo A, Virtanen A, O’Donoghue AJ, Del Rio Flores A, Garmendia AE, Pineda-Lucena A, Panganiban AT, Samantha A, Chatterjee AK, Haas AL, Paparella AS, John ALS, Prince A, ElSheikh A, Apfel AM, Colomba A, O’Dea A, Diallo BN, Ribeiro BMRM, Bailey-Elkin BA, Edelman BL, Liou B, Perry B, Chua BSK, Kováts B, Englinger B, Balakrishnan B, Gong B, Agianian B, Pressly B, Salas BPM, Duggan BM, Geisbrecht BV, Dymock BW, Morten BC, Hammock BD, Mota BEF, Dickinson BC, Fraser C, Lempicki C, Novina CD, Torner C, Ballatore C, Bon C, Chapman CJ, Partch CL, Chaton CT, Huang C, Yang CY, Kahler CM, Karan C, Keller C, Dieck CL, Huimei C, Liu C, Peltier C, Mantri CK, Kemet CM, Müller CE, Weber C, Zeina CM, Muli CS, Morisseau C, Alkan C, Reglero C, Loy CA, Wilson CM, Myhr C, Arrigoni C, Paulino C, Santiago C, Luo D, Tumes DJ, Keedy DA, Lawrence DA, Chen D, Manor D, Trader DJ, Hildeman DA, Drewry DH, Dowling DJ, Hosfield DJ, Smith DM, Moreira D, Siderovski DP, Shum D, Krist DT, Riches DWH, Ferraris DM, Anderson DH, Coombe DR, Welsbie DS, Hu D, Ortiz D, Alramadhani D, Zhang D, Chaudhuri D, Slotboom DJ, Ronning DR, Lee D, Dirksen D, Shoue DA, Zochodne DW, Krishnamurthy D, Duncan D, Glubb DM, Gelardi ELM, Hsiao EC, Lynn EG, Silva EB, Aguilera E, Lenci E, Abraham ET, Lama E, Mameli E, Leung E, Christensen EM, Mason ER, Petretto E, Trakhtenberg EF, Rubin EJ, Strauss E, Thompson EW, Cione E, Lisabeth EM, Fan E, Kroon EG, Jo E, García-Cuesta EM, Glukhov E, Gavathiotis E, Yu F, Xiang F, Leng F, Wang F, Ingoglia F, van den Akker F, Borriello F, Vizeacoumar FJ, Luh F, Buckner FS, Vizeacoumar FS, Bdira FB, Svensson F, Rodriguez GM, Bognár G, Lembo G, Zhang G, Dempsey G, Eitzen G, Mayer G, Greene GL, Garcia GA, Lukacs GL, Prikler G, Parico GCG, Colotti G, De Keulenaer G, Cortopassi G, Roti G, Girolimetti G, Fiermonte G, Gasparre G, Leuzzi G, Dahal G, Michlewski G, Conn GL, Stuchbury GD, Bowman GR, Popowicz GM, Veit G, de Souza GE, Akk G, Caljon G, Alvarez G, Rucinski G, Lee G, Cildir G, Li H, Breton HE, Jafar-Nejad H, Zhou H, Moore HP, Tilford H, Yuan H, Shim H, Wulff H, Hoppe H, Chaytow H, Tam HK, Van Remmen H, Xu H, Debonsi HM, Lieberman HB, Jung H, Fan HY, Feng H, Zhou H, Kim HJ, Greig IR, Caliandro I, Corvo I, Arozarena I, Mungrue IN, Verhamme IM, Qureshi IA, Lotsaris I, Cakir I, Perry JJP, Kwiatkowski J, Boorman J, Ferreira J, Fries J, Kratz JM, Miner J, Siqueira-Neto JL, Granneman JG, Ng J, Shorter J, Voss JH, Gebauer JM, Chuah J, Mousa JJ, Maynes JT, Evans JD, Dickhout J, MacKeigan JP, Jossart JN, Zhou J, Lin J, Xu J, Wang J, Zhu J, Liao J, Xu J, Zhao J, Lin J, Lee J, Reis J, Stetefeld J, Bruning JB, Bruning JB, Coles JG, Tanner JJ, Pascal JM, So J, Pederick JL, Costoya JA, Rayman JB, Maciag JJ, Nasburg JA, Gruber JJ, Finkelstein JM, Watkins J, Rodríguez-Frade JM, Arias JAS, Lasarte JJ, Oyarzabal J, Milosavljevic J, Cools J, Lescar J, Bogomolovas J, Wang J, Kee JM, Kee JM, Liao J, Sistla JC, Abrahão JS, Sishtla K, Francisco KR, Hansen KB, Molyneaux KA, Cunningham KA, Martin KR, Gadar K, Ojo KK, Wong KS, Wentworth KL, Lai K, Lobb KA, Hopkins KM, Parang K, Machaca K, Pham K, Ghilarducci K, Sugamori KS, McManus KJ, Musta K, Faller KME, Nagamori K, Mostert KJ, Korotkov KV, Liu K, Smith KS, Sarosiek K, Rohde KH, Kim KK, Lee KH, Pusztai L, Lehtiö L, Haupt LM, Cowen LE, Byrne LJ, Su L, Wert-Lamas L, Puchades-Carrasco L, Chen L, Malkas LH, Zhuo L, Hedstrom L, Hedstrom L, Walensky LD, Antonelli L, Iommarini L, Whitesell L, Randall LM, Fathallah MD, Nagai MH, Kilkenny ML, Ben-Johny M, Lussier MP, Windisch MP, Lolicato M, Lolli ML, Vleminckx M, Caroleo MC, Macias MJ, Valli M, Barghash MM, Mellado M, Tye MA, Wilson MA, Hannink M, Ashton MR, Cerna MVC, Giorgis M, Safo MK, Maurice MS, McDowell MA, Pasquali M, Mehedi M, Serafim MSM, Soellner MB, Alteen MG, Champion MM, Skorodinsky M, O’Mara ML, Bedi M, Rizzi M, Levin M, Mowat M, Jackson MR, Paige M, Al-Yozbaki M, Giardini MA, Maksimainen MM, De Luise M, Hussain MS, Christodoulides M, Stec N, Zelinskaya N, Van Pelt N, Merrill NM, Singh N, Kootstra NA, Singh N, Gandhi NS, Chan NL, Trinh NM, Schneider NO, Matovic N, Horstmann N, Longo N, Bharambe N, Rouzbeh N, Mahmoodi N, Gumede NJ, Anastasio NC, Khalaf NB, Rabal O, Kandror O, Escaffre O, Silvennoinen O, Bishop OT, Iglesias P, Sobrado P, Chuong P, O’Connell P, Martin-Malpartida P, Mellor P, Fish PV, Moreira POL, Zhou P, Liu P, Liu P, Wu P, Agogo-Mawuli P, Jones PL, Ngoi P, Toogood P, Ip P, von Hundelshausen P, Lee PH, Rowswell-Turner RB, Balaña-Fouce R, Rocha REO, Guido RVC, Ferreira RS, Agrawal RK, Harijan RK, Ramachandran R, Verma R, Singh RK, Tiwari RK, Mazitschek R, Koppisetti RK, Dame RT, Douville RN, Austin RC, Taylor RE, Moore RG, Ebright RH, Angell RM, Yan R, Kejriwal R, Batey RA, Blelloch R, Vandenberg RJ, Hickey RJ, Kelm RJ, Lake RJ, Bradley RK, Blumenthal RM, Solano R, Gierse RM, Viola RE, McCarthy RR, Reguera RM, Uribe RV, do Monte-Neto RL, Gorgoglione R, Cullinane RT, Katyal S, Hossain S, Phadke S, Shelburne SA, Geden SE, Johannsen S, Wazir S, Legare S, Landfear SM, Radhakrishnan SK, Ammendola S, Dzhumaev S, Seo SY, Li S, Zhou S, Chu S, Chauhan S, Maruta S, Ashkar SR, Shyng SL, Conticello SG, Buroni S, Garavaglia S, White SJ, Zhu S, Tsimbalyuk S, Chadni SH, Byun SY, Park S, Xu SQ, Banerjee S, Zahler S, Espinoza S, Gustincich S, Sainas S, Celano SL, Capuzzi SJ, Waggoner SN, Poirier S, Olson SH, Marx SO, Van Doren SR, Sarilla S, Brady-Kalnay SM, Dallman S, Azeem SM, Teramoto T, Mehlman T, Swart T, Abaffy T, Akopian T, Haikarainen T, Moreda TL, Ikegami T, Teixeira TR, Jayasinghe TD, Gillingwater TH, Kampourakis T, Richardson TI, Herdendorf TJ, Kotzé TJ, O’Meara TR, Corson TW, Hermle T, Ogunwa TH, Lan T, Su T, Banjo T, O’Mara TA, Chou T, Chou TF, Baumann U, Desai UR, Pai VP, Thai VC, Tandon V, Banerji V, Robinson VL, Gunasekharan V, Namasivayam V, Segers VFM, Maranda V, Dolce V, Maltarollo VG, Scoffone VC, Woods VA, Ronchi VP, Van Hung Le V, Clayton WB, Lowther WT, Houry WA, Li W, Tang W, Zhang W, Van Voorhis WC, Donaldson WA, Hahn WC, Kerr WG, Gerwick WH, Bradshaw WJ, Foong WE, Blanchet X, Wu X, Lu X, Qi X, Xu X, Yu X, Qin X, Wang X, Yuan X, Zhang X, Zhang YJ, Hu Y, Aldhamen YA, Chen Y, Li Y, Sun Y, Zhu Y, Gupta YK, Pérez-Pertejo Y, Li Y, Tang Y, He Y, Tse-Dinh YC, Sidorova YA, Yen Y, Li Y, Frangos ZJ, Chung Z, Su Z, Wang Z, Zhang Z, Liu Z, Inde Z, Artía Z, Heifets A. AI is a viable alternative to high throughput screening: a 318-target study. Sci Rep 2024; 14:7526. [PMID: 38565852 PMCID: PMC10987645 DOI: 10.1038/s41598-024-54655-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 02/15/2024] [Indexed: 04/04/2024] Open
Abstract
High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, high-quality X-ray crystal structures, or manual cherry-picking of compounds. We show that the molecules selected by the AtomNet® model are novel drug-like scaffolds rather than minor modifications to known bioactive compounds. Our empirical results suggest that computational methods can substantially replace HTS as the first step of small-molecule drug discovery.
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Holmes SG, Desai UR. Assessing Genetic Algorithm-Based Docking Protocols for Prediction of Heparin Oligosaccharide Binding Geometries onto Proteins. Biomolecules 2023; 13:1633. [PMID: 38002315 PMCID: PMC10669598 DOI: 10.3390/biom13111633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Although molecular docking has evolved dramatically over the years, its application to glycosaminoglycans (GAGs) has remained challenging because of their intrinsic flexibility, highly anionic character and rather ill-defined site of binding on proteins. GAGs have been treated as either fully "rigid" or fully "flexible" in molecular docking. We reasoned that an intermediate semi-rigid docking (SRD) protocol may be better for the recapitulation of native heparin/heparan sulfate (Hp/HS) topologies. Herein, we study 18 Hp/HS-protein co-complexes containing chains from disaccharide to decasaccharide using genetic algorithm-based docking with rigid, semi-rigid, and flexible docking protocols. Our work reveals that rigid and semi-rigid protocols recapitulate native poses for longer chains (5→10 mers) significantly better than the flexible protocol, while 2→4-mer poses are better predicted using the semi-rigid approach. More importantly, the semi-rigid docking protocol is likely to perform better when no crystal structure information is available. We also present a new parameter for parsing selective versus non-selective GAG-protein systems, which relies on two computational parameters including consistency of binding (i.e., RMSD) and docking score (i.e., GOLD Score). The new semi-rigid protocol in combination with the new computational parameter is expected to be particularly useful in high-throughput screening of GAG sequences for identifying promising druggable targets as well as drug-like Hp/HS sequences.
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Affiliation(s)
- Samuel G. Holmes
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA;
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, 800 E. Leigh Street, Suite 212, Richmond, VA 23219, USA
| | - Umesh R. Desai
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA;
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, 800 E. Leigh Street, Suite 212, Richmond, VA 23219, USA
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Pradhan AK, Modi J, Maji S, Kumar A, Bhoopathi P, Mannangatti P, Guo C, Afosah DK, Mochel MC, Mukhopadhyay ND, Kirkwood JM, Wang XY, Desai UR, Sarkar D, Emdad L, Das SK, Fisher PB. Dual Targeting of the PDZ1 and PDZ2 Domains of MDA-9/Syntenin Inhibits Melanoma Metastasis. Mol Cancer Ther 2023; 22:1115-1127. [PMID: 37721536 DOI: 10.1158/1535-7163.mct-22-0653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 04/14/2023] [Accepted: 06/27/2023] [Indexed: 09/19/2023]
Abstract
Genome-wide gene expression analysis and animal modeling indicate that melanoma differentiation associated gene-9 (mda-9, Syntenin, Syndecan binding protein, referred to as MDA-9/Syntenin) positively regulates melanoma metastasis. The MDA-9/Syntenin protein contains two tandem PDZ domains serving as a nexus for interactions with multiple proteins that initiate transcription of metastasis-associated genes. Although targeting either PDZ domain abrogates signaling and prometastatic phenotypes, the integrity of both domains is critical for full biological function. Fragment-based drug discovery and NMR identified PDZ1i, an inhibitor of the PDZ1 domain that effectively blocks cancer invasion in vitro and in vivo in multiple experimental animal models. To maximize disruption of MDA-9/Syntenin signaling, an inhibitor has now been developed that simultaneously binds and blocks activity of both PDZ domains. PDZ1i was joined to the second PDZ binding peptide (TNYYFV) with a PEG linker, resulting in PDZ1i/2i (IVMT-Rx-3) that engages both PDZ domains of MDA-9/Syntenin. IVMT-Rx-3 blocks MDA-9/Syntenin interaction with Src, reduces NF-κB activation, and inhibits MMP-2/MMP-9 expression, culminating in repression of melanoma metastasis. The in vivo antimetastatic properties of IVMT-Rx-3 are enhanced when combined with an immune-checkpoint inhibitor. Collectively, our results support the feasibility of engineering MDA-9 dual-PDZ inhibitors with enhanced antimetastatic activities and applications of IVMT-Rx-3 for developing novel therapeutic strategies effectively targeting melanoma and in principle, a broad spectrum of human cancers that also overexpress MDA-9/Syntenin.
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Affiliation(s)
- Anjan K Pradhan
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
| | - Jinkal Modi
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
| | - Santanu Maji
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
| | - Amit Kumar
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
| | - Praveen Bhoopathi
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
| | - Padmanabhan Mannangatti
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
| | - Chunqing Guo
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
- VCU Institute of Molecular Medicine, Massey Comprehensive Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
| | - Daniel K Afosah
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia
| | - Mark C Mochel
- Department of Pathology, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
| | - Nitai D Mukhopadhyay
- Department of Biostatistics, Virginia Commonwealth University, Richmond, Virginia
| | - John M Kirkwood
- Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Xiang-Yang Wang
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
- VCU Institute of Molecular Medicine, Massey Comprehensive Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
| | - Umesh R Desai
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia
| | - Devanand Sarkar
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
- VCU Institute of Molecular Medicine, Massey Comprehensive Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
| | - Luni Emdad
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
- VCU Institute of Molecular Medicine, Massey Comprehensive Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
| | - Swadesh K Das
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
- VCU Institute of Molecular Medicine, Massey Comprehensive Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
| | - Paul B Fisher
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
- VCU Institute of Molecular Medicine, Massey Comprehensive Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
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Kellogg GE, Cen Y, Dukat M, Ellis KC, Guo Y, Li J, May AE, Safo MK, Zhang S, Zhang Y, Desai UR. Merging cultures and disciplines to create a drug discovery ecosystem at Virginia commonwealth university: Medicinal chemistry, structural biology, molecular and behavioral pharmacology and computational chemistry. SLAS Discov 2023; 28:255-269. [PMID: 36863508 PMCID: PMC10619687 DOI: 10.1016/j.slasd.2023.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/10/2023] [Accepted: 02/21/2023] [Indexed: 03/04/2023]
Abstract
The Department of Medicinal Chemistry, together with the Institute for Structural Biology, Drug Discovery and Development, at Virginia Commonwealth University (VCU) has evolved, organically with quite a bit of bootstrapping, into a unique drug discovery ecosystem in response to the environment and culture of the university and the wider research enterprise. Each faculty member that joined the department and/or institute added a layer of expertise, technology and most importantly, innovation, that fertilized numerous collaborations within the University and with outside partners. Despite moderate institutional support with respect to a typical drug discovery enterprise, the VCU drug discovery ecosystem has built and maintained an impressive array of facilities and instrumentation for drug synthesis, drug characterization, biomolecular structural analysis and biophysical analysis, and pharmacological studies. Altogether, this ecosystem has had major impacts on numerous therapeutic areas, such as neurology, psychiatry, drugs of abuse, cancer, sickle cell disease, coagulopathy, inflammation, aging disorders and others. Novel tools and strategies for drug discovery, design and development have been developed at VCU in the last five decades; e.g., fundamental rational structure-activity relationship (SAR)-based drug design, structure-based drug design, orthosteric and allosteric drug design, design of multi-functional agents towards polypharmacy outcomes, principles on designing glycosaminoglycans as drugs, and computational tools and algorithms for quantitative SAR (QSAR) and understanding the roles of water and the hydrophobic effect.
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Affiliation(s)
- Glen E Kellogg
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, 23298-0540, USA.
| | - Yana Cen
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, 23298-0540, USA
| | - Malgorzata Dukat
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, 23298-0540, USA
| | - Keith C Ellis
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, 23298-0540, USA
| | - Youzhong Guo
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, 23298-0540, USA
| | - Jiong Li
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, 23298-0540, USA
| | - Aaron E May
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, 23298-0540, USA
| | - Martin K Safo
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, 23298-0540, USA
| | - Shijun Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, 23298-0540, USA
| | - Yan Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, 23298-0540, USA
| | - Umesh R Desai
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, 23298-0540, USA.
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6
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Sankaranarayanan NV, Sistla S, Nagarajan B, Chittum JE, Lau JTY, Desai UR. Computational studies on glycosaminoglycan recognition of sialyl transferases. Glycobiology 2023; 33:579-590. [PMID: 37171590 PMCID: PMC10426320 DOI: 10.1093/glycob/cwad040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/03/2023] [Accepted: 05/11/2023] [Indexed: 05/13/2023] Open
Abstract
Despite decades of research, glycosaminoglycans (GAGs) have not been known to interact with sialyl transferases (STs). Using our in-house combinatorial virtual library screening (CVLS) technology, we studied seven human isoforms, including ST6GAL1, ST6GAL2, ST3GAL1, ST3GAL3, ST3GAL4, ST3GAL5, and ST3GAL6, and predicted that GAGs, especially heparan sulfate (HS), are likely to differentially bind to STs. Exhaustive CVLS and molecular dynamics studies suggested that the common hexasaccharide sequence of HS preferentially recognized ST6GAL1 in a site overlapping the binding site of the donor substrate CMP-Sia. Interestingly, CVLS did not ascribe any special role for the rare 3-O-sulfate modification of HS in ST6GAL1 recognition. The computational predictions were tested using spectrofluorimetric studies, which confirmed preferential recognition of HS over other GAGs. A classic chain length-dependent binding of GAGs to ST6GAL1 was observed with polymeric HS displaying a tight affinity of ~65 nM. Biophysical studies also confirmed a direct competition between CMP-Sia and an HS oligosaccharide and CS polysaccharide for binding to ST6GAL1. Overall, our novel observation that GAGs bind to ST6GAL1 with high affinity and compete with the donor substrate is likely to be important because modulation of sialylation of glycan substrates on cells has considerable physiological/pathological consequences. Our work also brings forth the possibility of developing GAG-based chemical probes of ST6GAL1.
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Affiliation(s)
- Nehru Viji Sankaranarayanan
- Department of Medicinal Chemistry, Virginia Commonwealth University, Virginia 23298, Richmond, USA
- Drug Discovery and Development, Virginia Commonwealth University, Institute for Structural Biology, Virginia 23219, Richmond, USA
| | - Srinivas Sistla
- Department of Medicinal Chemistry, Virginia Commonwealth University, Virginia 23298, Richmond, USA
- Drug Discovery and Development, Virginia Commonwealth University, Institute for Structural Biology, Virginia 23219, Richmond, USA
| | - Balaji Nagarajan
- Department of Medicinal Chemistry, Virginia Commonwealth University, Virginia 23298, Richmond, USA
- Drug Discovery and Development, Virginia Commonwealth University, Institute for Structural Biology, Virginia 23219, Richmond, USA
| | - John E Chittum
- Department of Medicinal Chemistry, Virginia Commonwealth University, Virginia 23298, Richmond, USA
- Drug Discovery and Development, Virginia Commonwealth University, Institute for Structural Biology, Virginia 23219, Richmond, USA
| | - Joseph T Y Lau
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo 14263, NY, USA
| | - Umesh R Desai
- Department of Medicinal Chemistry, Virginia Commonwealth University, Virginia 23298, Richmond, USA
- Drug Discovery and Development, Virginia Commonwealth University, Institute for Structural Biology, Virginia 23219, Richmond, USA
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7
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Afosah DK, Fayyad RM, Puliafico VR, Merrell S, Langmia EK, Diagne SR, Al-Horani RA, Desai UR. Homogeneous, Synthetic, Non-Saccharide Glycosaminoglycan Mimetics as Potent Inhibitors of Human Cathepsin G. Biomolecules 2023; 13:760. [PMID: 37238630 PMCID: PMC10216581 DOI: 10.3390/biom13050760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 04/25/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023] Open
Abstract
Cathepsin G (CatG) is a pro-inflammatory neutrophil serine protease that is important for host defense, and has been implicated in several inflammatory disorders. Hence, inhibition of CatG holds much therapeutic potential; however, only a few inhibitors have been identified to date, and none have reached clinical trials. Of these, heparin is a well-known inhibitor of CatG, but its heterogeneity and bleeding risk reduce its clinical potential. We reasoned that synthetic small mimetics of heparin, labeled as non-saccharide glycosaminoglycan mimetics (NSGMs), would exhibit potent CatG inhibition while being devoid of bleeding risks associated with heparin. Hence, we screened a focused library of 30 NSGMs for CatG inhibition using a chromogenic substrate hydrolysis assay and identified nano- to micro-molar inhibitors with varying levels of efficacy. Of these, a structurally-defined, octasulfated di-quercetin NSGM 25 inhibited CatG with a potency of ~50 nM. NSGM 25 binds to CatG in an allosteric site through an approximately equal contribution of ionic and nonionic forces. Octasulfated 25 exhibits no impact on human plasma clotting, suggesting minimal bleeding risk. Considering that octasulfated 25 also potently inhibits two other pro-inflammatory proteases, human neutrophil elastase and human plasmin, the current results imply the possibility of a multi-pronged anti-inflammatory approach in which these proteases are likely to simultaneously likely combat important conditions, e.g., rheumatoid arthritis, emphysema, or cystic fibrosis, with minimal bleeding risk.
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Affiliation(s)
- Daniel K. Afosah
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA; (R.M.F.)
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Rawan M. Fayyad
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA; (R.M.F.)
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Valerie R. Puliafico
- Department of Chemistry and Biochemistry, Washington and Lee University, Lexington, VA 24450, USA
| | - Spencer Merrell
- Department of Chemistry and Biochemistry, Washington and Lee University, Lexington, VA 24450, USA
| | - Eltice K. Langmia
- Department of Chemistry and Biochemistry, Washington and Lee University, Lexington, VA 24450, USA
| | - Sophie R. Diagne
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Rami A. Al-Horani
- Division of Basic Pharmaceutical Sciences, College of Pharmacy, Xavier University of Louisiana, New Orleans, LA 70125, USA
| | - Umesh R. Desai
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA; (R.M.F.)
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA
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8
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Abdelfadiel E, Gunta R, Villuri BK, Afosah DK, Sankaranarayanan NV, Desai UR. Designing Smaller, Synthetic, Functional Mimetics of Sulfated Glycosaminoglycans as Allosteric Modulators of Coagulation Factors. J Med Chem 2023; 66:4503-4531. [PMID: 37001055 PMCID: PMC10108365 DOI: 10.1021/acs.jmedchem.3c00132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Indexed: 04/03/2023]
Abstract
Natural glycosaminoglycans (GAGs) are arguably the most diverse collection of natural products. Unfortunately, this bounty of structures remains untapped. Decades of research has realized only one GAG-like synthetic, small-molecule drug, fondaparinux. This represents an abysmal output because GAGs present a frontier that few medicinal chemists, and even fewer pharmaceutical companies, dare to undertake. GAGs are heterogeneous, polymeric, polydisperse, highly water soluble, synthetically challenging, too rapidly cleared, and difficult to analyze. Additionally, GAG binding to proteins is not very selective and GAG-binding sites are shallow. This Perspective attempts to transform this negative view into a much more promising one by highlighting recent advances in GAG mimetics. The Perspective focuses on the principles used in the design/discovery of drug-like, synthetic, sulfated small molecules as allosteric modulators of coagulation factors, such as antithrombin, thrombin, and factor XIa. These principles will also aid the design/discovery of sulfated agents against cancer, inflammation, and microbial infection.
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Affiliation(s)
- Elsamani
I. Abdelfadiel
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
| | - Rama Gunta
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Bharath Kumar Villuri
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Daniel K. Afosah
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Nehru Viji Sankaranarayanan
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Umesh R. Desai
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
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9
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Ponnuraj N, Akbar H, Arrington JV, Spatz SJ, Nagarajan B, Desai UR, Jarosinski KW. The alphaherpesvirus conserved pUS10 is important for natural infection and its expression is regulated by the conserved Herpesviridae protein kinase (CHPK). PLoS Pathog 2023; 19:e1010959. [PMID: 36749787 PMCID: PMC9946255 DOI: 10.1371/journal.ppat.1010959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 02/22/2023] [Accepted: 01/30/2023] [Indexed: 02/08/2023] Open
Abstract
Conserved Herpesviridae protein kinases (CHPK) are conserved among all members of the Herpesviridae. Herpesviruses lacking CHPK propagate in cell culture at varying degrees, depending on the virus and cell culture system. CHPK is dispensable for Marek's disease herpesvirus (MDV) replication in cell culture and experimental infection in chickens; however, CHPK-particularly its kinase activity-is essential for horizontal transmission in chickens, also known as natural infection. To address the importance of CHPK during natural infection in chickens, we used liquid chromatography-tandem mass spectrometry (LC-MS/MS) based proteomics of samples collected from live chickens. Comparing modification of viral proteins in feather follicle epithelial (FFE) cells infected with wildtype or a CHPK-null virus, we identified the US10 protein (pUS10) as a potential target for CHPK in vivo. When expression of pUS10 was evaluated in cell culture and in FFE skin cells during in vivo infection, pUS10 was severely reduced or abrogated in cells infected with CHPK mutant or CHPK-null viruses, respectively, indicating a potential role for pUS10 in transmission. To test this hypothesis, US10 was deleted from the MDV genome, and the reconstituted virus was tested for replication, horizontal transmission, and disease induction. Our results showed that removal of US10 had no effect on the ability of MDV to transmit in experimentally infected chickens, but disease induction in naturally infected chickens was significantly reduced. These results show CHPK is necessary for pUS10 expression both in cell culture and in the host, and pUS10 is important for disease induction during natural infection.
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Affiliation(s)
- Nagendraprabhu Ponnuraj
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Haji Akbar
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Justine V. Arrington
- Protein Sciences Facility, Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, Illinois, United States of America
| | - Stephen J. Spatz
- US National Poultry Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Athens, Georgia, United States of America
| | - Balaji Nagarajan
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Umesh R. Desai
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Keith W. Jarosinski
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
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10
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Morla S, Ravikumar O, O’Hara C, Boothello R, Vera A, Abdelfadiel EI, Fayyad R, Afosah DK, Sharon C, Fernandez L, Shah SA, Patel BB, Desai UR. Designing Synthetic, Sulfated Glycosaminoglycan Mimetics That Are Orally Bioavailable and Exhibiting In Vivo Anticancer Activity. J Med Chem 2023; 66:1321-1338. [PMID: 36634271 PMCID: PMC9884082 DOI: 10.1021/acs.jmedchem.2c01511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Indexed: 01/13/2023]
Abstract
Sulfated glycosaminoglycans (GAGs), or synthetic mimetics thereof, are not favorably viewed as orally bioavailable drugs owing to their high number of anionic sulfate groups. Devising an approach for oral delivery of such highly sulfated molecules would be very useful. This work presents the concept that conjugating cholesterol to synthetic sulfated GAG mimetics enables oral delivery. A focused library of sulfated GAG mimetics was synthesized and found to inhibit the growth of a colorectal cancer cell line under spheroid conditions with a wide range of potencies ( 0.8 to 46 μM). Specific analogues containing cholesterol, either alone or in combination with clinical utilized drugs, exhibited pronounced in vivo anticancer potential with intraperitoneal as well as oral administration, as assessed by ex vivo tertiary and quaternary spheroid growth, cancer stem cell (CSC) markers, and/or self-renewal factors. Overall, cholesterol derivatization of highly sulfated GAG mimetics affords an excellent approach for engineering oral activity.
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Affiliation(s)
- Shravan Morla
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
| | - Ongolu Ravikumar
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
| | - Connor O’Hara
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
| | - Rio Boothello
- Division
of Hematology, Oncology and Palliative Care, Department of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Alberto Vera
- Hunter
Holmes McGuire VA Medical Center, Richmond, Virginia 23249, United States
| | - Elsamani I. Abdelfadiel
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
| | - Rawan Fayyad
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
| | - Daniel K. Afosah
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
| | - Chetna Sharon
- Hunter
Holmes McGuire VA Medical Center, Richmond, Virginia 23249, United States
| | - Leopoldo Fernandez
- Hunter
Holmes McGuire VA Medical Center, Richmond, Virginia 23249, United States
- Massey
Cancer Center, Richmond, Virginia 23298, United States
- Division
of Surgical Oncology, Department of Surgery, Hunter Holmes McGuire VA Medical Center, Richmond, Virginia 23249, United States
| | - Syed Ammer Shah
- Hunter
Holmes McGuire VA Medical Center, Richmond, Virginia 23249, United States
- Massey
Cancer Center, Richmond, Virginia 23298, United States
- Division
of Surgical Oncology, Department of Surgery, Hunter Holmes McGuire VA Medical Center, Richmond, Virginia 23249, United States
| | - Bhaumik B. Patel
- Division
of Hematology, Oncology and Palliative Care, Department of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298, United States
- Hunter
Holmes McGuire VA Medical Center, Richmond, Virginia 23249, United States
- Massey
Cancer Center, Richmond, Virginia 23298, United States
| | - Umesh R. Desai
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
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11
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Boothello RS, Sankaranarayanan NV, Sistla JC, Nagarajan B, Sharon C, Chittum JE, Niyaz RY, Roy S, Nandi A, O'Hara CP, Navaz Gangji R, Afosah DK, Ongolu R, Patel BB, Desai UR. Glycan Modulation of Insulin‐like Growth Factor‐1 Receptor. Angew Chem Int Ed Engl 2022; 61:e202211320. [PMID: 36205924 PMCID: PMC9712175 DOI: 10.1002/anie.202211320] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Indexed: 11/07/2022]
Abstract
The insulin-like growth factor-1 receptor (IGF-1R) is a receptor tyrosine kinase (RTK) that plays critical roles in cancer. Microarray, computational, thermodynamic, and cellular imaging studies reveal that activation of IGF-1R by its cognate ligand IGF1 is inhibited by shorter, soluble heparan sulfate (HS) sequences (e.g., HS06), whereas longer polymeric chains do not inhibit the RTK, a phenomenon directly opposed to the traditional relationship known for GAG-protein systems. The inhibition arises from smaller oligosaccharides binding in a unique pocket in the IGF-1R ectodomain, which competes with the natural cognate ligand IGF1. This work presents a highly interesting observation on preferential and competing inhibition of IGF-1R by smaller sequences, whereas polysaccharides are devoid of this function. These insights will be of major value to glycobiologists and anti-cancer drug discoverers.
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Affiliation(s)
- Rio S Boothello
- Hunter Holmes McGuire Richmond VA Medical Center: Hunter Holmes McGuire VA Medical Center Internal Medicine UNITED STATES
| | | | - Jyothi C Sistla
- Virginia Commonwealth University Medicinal Chemistry UNITED STATES
| | - Balaji Nagarajan
- Virginia Commonwealth University Medicinal Chemistry UNITED STATES
| | - Chetna Sharon
- Hunter Holmes McGuire Richmond VA Medical Center: Hunter Holmes McGuire VA Medical Center Internal Medicine UNITED STATES
| | - John E Chittum
- Virginia Commonwealth University Medicinal Chemistry UNITED STATES
| | - Rabiya Y Niyaz
- Hunter Holmes McGuire Richmond VA Medical Center: Hunter Holmes McGuire VA Medical Center Internal Medicine UNITED STATES
| | - Swarnali Roy
- Virginia Commonwealth University Medicinal Chemistry UNITED STATES
| | - Aditi Nandi
- Virginia Commonwealth University School of Medicine Internal Medicine UNITED STATES
| | - Connor P O'Hara
- Virginia Commonwealth University Medicinal Chemistry UNITED STATES
| | | | - Daniel K Afosah
- Virginia Commonwealth University Medicinal Chemistry UNITED STATES
| | - Ravikumar Ongolu
- Virginia Commonwealth University Medicinal Chemistry UNITED STATES
| | - Bhaumik B Patel
- Virginia Commonwealth University School of Medicine Division of Hematology, Oncology and Palliative Care, Department of Internal Medicine UNITED STATES
| | - Umesh R. Desai
- Virginia Commonwealth University Institute for Structural Biology and Drug Design 800 East Leigh Street #212 23219 Richmond UNITED STATES
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12
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Boothello RS, Sankaranarayanan NV, Sistla JC, Nagarajan B, Sharon C, Chittum JE, Niyaz RY, Roy S, Nandi A, O'Hara CP, Navaz Gangji R, Afosah DK, Ongolu R, Patel BB, Desai UR. Glycan Modulation of Insulin‐like Growth Factor‐1 Receptor. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202211320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Rio S Boothello
- Hunter Holmes McGuire Richmond VA Medical Center: Hunter Holmes McGuire VA Medical Center Internal Medicine UNITED STATES
| | | | - Jyothi C Sistla
- Virginia Commonwealth University Medicinal Chemistry UNITED STATES
| | - Balaji Nagarajan
- Virginia Commonwealth University Medicinal Chemistry UNITED STATES
| | - Chetna Sharon
- Hunter Holmes McGuire Richmond VA Medical Center: Hunter Holmes McGuire VA Medical Center Internal Medicine UNITED STATES
| | - John E Chittum
- Virginia Commonwealth University Medicinal Chemistry UNITED STATES
| | - Rabiya Y Niyaz
- Hunter Holmes McGuire Richmond VA Medical Center: Hunter Holmes McGuire VA Medical Center Internal Medicine UNITED STATES
| | - Swarnali Roy
- Virginia Commonwealth University Medicinal Chemistry UNITED STATES
| | - Aditi Nandi
- Virginia Commonwealth University School of Medicine Internal Medicine UNITED STATES
| | - Connor P O'Hara
- Virginia Commonwealth University Medicinal Chemistry UNITED STATES
| | | | - Daniel K Afosah
- Virginia Commonwealth University Medicinal Chemistry UNITED STATES
| | - Ravikumar Ongolu
- Virginia Commonwealth University Medicinal Chemistry UNITED STATES
| | - Bhaumik B Patel
- Virginia Commonwealth University School of Medicine Division of Hematology, Oncology and Palliative Care, Department of Internal Medicine UNITED STATES
| | - Umesh R. Desai
- Virginia Commonwealth University Institute for Structural Biology and Drug Design 800 East Leigh Street #212 23219 Richmond UNITED STATES
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13
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Holmes SG, Nagarajan B, Desai UR. 3- O-Sulfation induces sequence-specific compact topologies in heparan sulfate that encode a dynamic sulfation code. Comput Struct Biotechnol J 2022; 20:3884-3898. [PMID: 35891779 PMCID: PMC9309406 DOI: 10.1016/j.csbj.2022.07.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/05/2022] [Accepted: 07/05/2022] [Indexed: 11/17/2022] Open
Abstract
Heparan sulfate (HS) is arguably the most diverse linear biopolymer that is known to modulate hundreds of proteins. Whereas the configurational and conformational diversity of HS is well established in terms of varying sulfation patterns and iduronic acid (IdoA) puckers, a linear helical topology resembling a cylindrical rod is the only topology thought to be occupied by the biopolymer. We reasoned that 3-O-sulfation, a rare modification in natural HS, may induce novel topologies that contribute to selective recognition of proteins. In this work, we studied a library of 24 distinct HS hexasaccharides using molecular dynamics (MD). We discovered novel compact (C) topologies that are populated significantly by a unique group of 3-O-sulfated sequences containing IdoA residues. 3-O-sulfated sequences containing glucuronic acid (GlcA) residue and sequences devoid of 3-O-sulfate groups did not exhibit high levels of the C topology and primarily exhibited only the canonical linear (L) form. The C topology arises under dynamical conditions due to rotation around an IdoA → GlcN glycosidic linkage, especially in psi (Ψ) torsion. At an atomistic level, the L → C transformation is a multi-factorial phenomenon engineered to reduce like-charge repulsion, release one or more HS-bound water molecules, and organize a bi-dentate "IdoA-cation-IdoA" interaction. These forces also drive an L → C transformation in a 3-O-sulfated octasaccharide, which has shown evidence of the unique C topology in the co-crystallized state. The 3-O-sulfate-based generation of unique, sequence-specific, compact topologies indicate that natural HS encodes a dynamic sulfation code that could be exploited for selective recognition of target proteins.
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Affiliation(s)
- Samuel G. Holmes
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Balaji Nagarajan
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Umesh R. Desai
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA
- Corresponding author at: Institute for Structural Biology, Drug Discovery, and Development, 800 E. Leigh Street, Suite 212, Richmond, VA 23219, USA.
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14
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Chittum JE, Sankaranarayanan NV, O’Hara CP, Desai UR. On the Selectivity of Heparan Sulfate Recognition by SARS-CoV-2 Spike Glycoprotein. ACS Med Chem Lett 2021; 12:1710-1717. [PMID: 34786180 PMCID: PMC8525342 DOI: 10.1021/acsmedchemlett.1c00343] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 10/05/2021] [Indexed: 12/22/2022] Open
Abstract
SARS-CoV-2 infects human cells through its surface spike glycoprotein (SgP), which relies on host cell surface heparan sulfate (HS) proteoglycans that facilitate interaction with the ACE2 receptor. Targeting this process could lead to inhibitors of early steps in viral entry. Screening a microarray of 24 HS oligosaccharides against recombinant S1 and receptor-binding domain (RBD) proteins led to identification of only eight sequences as potent antagonists; results that were supported by detailed dual-filter computational studies. Competitive studies using the HS microarray suggested almost equivalent importance of IdoA2S-GlcNS6S and GlcNS3S structures, which were supported by affinity studies. Exhaustive virtual screening on a library of >93 000 sequences led to a novel pharmacophore with at least two 3-O-sulfated GlcN residues that can engineer unique selectivity in recognizing the RBD. This work puts forward the key structural motif in HS that should lead to potent and selective HS or HS-like agents against SARS-CoV-2.
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Affiliation(s)
- John E. Chittum
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
| | - Nehru Viji Sankaranarayanan
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
| | - Connor P. O’Hara
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
| | - Umesh R. Desai
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
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15
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Sankaranarayanan NV, Nagarajan B, Desai UR. Combinatorial Virtual Library Screening Study of Transforming Growth Factor-β2-Chondroitin Sulfate System. Int J Mol Sci 2021; 22:7542. [PMID: 34299163 PMCID: PMC8305211 DOI: 10.3390/ijms22147542] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/10/2021] [Accepted: 07/12/2021] [Indexed: 12/30/2022] Open
Abstract
Transforming growth factor-beta (TGF-β), a member of the TGF-β cytokine superfamily, is known to bind to sulfated glycosaminoglycans (GAGs), but the nature of this interaction remains unclear. In a recent study, we found that preterm human milk TGF-β2 is sequestered by chondroitin sulfate (CS) in its proteoglycan form. To understand the molecular basis of the TGF-β2-CS interaction, we utilized the computational combinatorial virtual library screening (CVLS) approach in tandem with molecular dynamics (MD) simulations. All possible CS oligosaccharides were generated in a combinatorial manner to give 24 di- (CS02), 192 tetra- (CS04), and 1536 hexa- (CS06) saccharides. This library of 1752 CS oligosaccharides was first screened against TGF-β2 using the dual filter CVLS algorithm in which the GOLDScore and root-mean-square-difference (RMSD) between the best bound poses were used as surrogate markers for in silico affinity and in silico specificity. CVLS predicted that both the chain length and level of sulfation are critical for the high affinity and high specificity recognition of TGF-β2. Interestingly, CVLS led to identification of two distinct sites of GAG binding on TGF-β2. CVLS also deduced the preferred composition of the high specificity hexasaccharides, which were further assessed in all-atom explicit solvent MD simulations. The MD results confirmed that both sites of binding form stable GAG-protein complexes. More specifically, the highly selective CS chains were found to engage the TGF-β2 monomer with high affinity. Overall, this work present key principles of recognition with regard to the TGF-β2-CS system. In the process, it led to the generation of the in silico library of all possible CS oligosaccharides, which can be used for advanced studies on other protein-CS systems. Finally, the study led to the identification of unique CS sequences that are predicted to selectively recognize TGF-β2 and may out-compete common natural CS biopolymers.
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Affiliation(s)
- Nehru Viji Sankaranarayanan
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA; (N.V.S.); (B.N.)
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Balaji Nagarajan
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA; (N.V.S.); (B.N.)
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Umesh R. Desai
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA; (N.V.S.); (B.N.)
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
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16
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O'Hara CP, Sankaranarayanan NV, Boothello RS, Patel BB, Desai UR. Abstract 1166: Structurally defined glycosaminoglycan mimetics exhibit preference for proteins of the growth factor family. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-1166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Heparan sulfate (HS), a glycosaminoglycans of considerable structural diversity, has been implicated in a wide-variety of complex roles including regulation of cell signaling. Unfortunately, homogeneous HS is a dream that will likely be unfulfilled this century. To combat this, our lab has synthesized an array of non-saccharide glycosaminoglycan mimetics (NSGMs) that act as structural and functional mimetics of HS. A key advantage of our NSGMs is homogeneity, which enables assessing selectivity for recognition of target proteins with a high degree of confidence. A second advantage is the quantitative measurement of the affinity of these interactions, which affords a detailed understanding of the forces governing recognition of different proteins. Previously, we have shown a lead NSGM named G2.2 as a potent and selective inhibitor of colorectal cancer stem cells (CSCs) through phenotypic in-vitro and in-vivo assays. To improve upon the drug-like properties of G2.2, cholesterol-modified analogs (G2C, G5C, G8C) were designed to enhance potency and selectivity for protein target(s). Although the hypothesis is that G2.2 and its lipidic analogs target a ligand and/or a receptor belonging to CSC-relevant growth factors, the preferred target, if any, remains to be identified. More importantly, the relative order of preference in-vitro and its use in predicted in-vivo activity remains to be determined. In this work, we have performed a comprehensive biophysical screening of a panel of potential growth factor targets using biophysical methods to determine binding affinities, followed by quantitative measurement of the relative forces of interactions involved in target recognition. Our studies are complemented by computational experiments that provide a foundation for thermodynamic studies. Analysis of our results indicate that these NSGMs preferentially recognize certain growth factor proteins, suggesting that appropriately designed HS mimetics can be tailored to modulate a particular tyrosine kinase receptor pathway. More importantly, our results convey the principle that despite the presence of multiple sulfate groups, HS mimetics can be designed to exhibit selectivity for certain growth factor proteins. In fact, the sulfate groups on our molecules may actually contribute to the selectivity and potency of recognition, two central principles for the development of drugs.
Citation Format: Connor P. O'Hara, Nehru V. Sankaranarayanan, Rio S. Boothello, Bhaumik B. Patel, Umesh R. Desai. Structurally defined glycosaminoglycan mimetics exhibit preference for proteins of the growth factor family [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1166.
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Pingali P, Wu YJ, Boothello R, Sharon C, Li H, Sistla S, Sankaranarayanan NV, Desai UR, Le AT, Doebele RC, Muldoon LL, Patel BB, Neuwelt A. High dose acetaminophen inhibits STAT3 and has free radical independent anti-cancer stem cell activity. Neoplasia 2021; 23:348-359. [PMID: 33640759 PMCID: PMC7920811 DOI: 10.1016/j.neo.2021.02.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/03/2021] [Accepted: 02/05/2021] [Indexed: 01/06/2023] Open
Abstract
High-dose acetaminophen (AAP) with delayed rescue using n-acetylcysteine (NAC), the FDA-approved antidote to AAP overdose, has demonstrated promising antitumor efficacy in early phase clinical trials. However, the mechanism of action (MOA) of AAP's anticancer effects remains elusive. Using clinically relevant AAP concentrations, we evaluated cancer stem cell (CSC) phenotype in vitro and in vivo in lung cancer and melanoma cells with diverse driver mutations. Associated mechanisms were also studied. Our results demonstrated that AAP inhibited 3D spheroid formation, self-renewal, and expression of CSC markers when human cancer cells were grown in serum-free CSC media. Similarly, anti-CSC activity was demonstrated in vivo in xenograft models - tumor formation following in vitro treatment and ex-vivo spheroid formation following in vivo treatment. Intriguingly, NAC, used to mitigate AAP's liver toxicity, did not rescue cells from AAP's anti-CSC effects, and AAP failed to reduce glutathione levels in tumor xenograft in contrast to mice liver tissue suggesting nonglutathione-related MOA. In fact, AAP mediates its anti-CSC effect via inhibition of STAT3. AAP directly binds to STAT3 with an affinity in the low micromolar range and a high degree of specificity for STAT3 relative to STAT1. These findings have high immediate translational significance concerning advancing AAP with NAC rescue to selectively rescue hepatotoxicity while inhibiting CSCs. The novel mechanism of selective STAT3 inhibition has implications for developing rational anticancer combinations and better patient selection (predictive biomarkers) for clinical studies and developing novel selective STAT3 inhibitors using AAP's molecular scaffold.
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Affiliation(s)
- Pavani Pingali
- Section of Hematology and Oncology, Medicine Service, Hunter Holmes McGuire VA Medical Center, Richmond, VA
| | | | - Rio Boothello
- Section of Hematology and Oncology, Medicine Service, Hunter Holmes McGuire VA Medical Center, Richmond, VA
| | - Chetna Sharon
- Section of Hematology and Oncology, Medicine Service, Hunter Holmes McGuire VA Medical Center, Richmond, VA
| | - Howard Li
- Department of Pulmonology, Hunter Holmes McGuire VA Medical Center, Richmond, VA; Department of Pulmonology, Virginia Commonwealth University Hospital, Richmond, VA
| | - Srinivas Sistla
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA
| | - Nehru Viji Sankaranarayanan
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA
| | - Umesh R Desai
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA; Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA
| | - Anh T Le
- Division of Medical Oncology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Robert C Doebele
- Division of Medical Oncology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | | | - Bhaumik B Patel
- Section of Hematology and Oncology, Medicine Service, Hunter Holmes McGuire VA Medical Center, Richmond, VA; Division of Hematology, Oncology, and Palliative care, Department of Medicine, and Massey Cancer Center, Virginia Commonwealth University. Richmond, VA.
| | - Alexander Neuwelt
- Section of Hematology and Oncology, Medicine Service, Hunter Holmes McGuire VA Medical Center, Richmond, VA; Division of Hematology, Oncology, and Palliative care, Department of Medicine, and Massey Cancer Center, Virginia Commonwealth University. Richmond, VA.
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Tiwari V, Tandon R, Sankaranarayanan NV, Beer JC, Kohlmeir EK, Swanson-Mungerson M, Desai UR. Preferential recognition and antagonism of SARS-CoV-2 spike glycoprotein binding to 3- O-sulfated heparan sulfate. bioRxiv 2020:2020.10.08.331751. [PMID: 33052337 PMCID: PMC7553162 DOI: 10.1101/2020.10.08.331751] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 is in immediate need of an effective antidote. Although the Spike glycoprotein (SgP) of SARS-CoV-2 has been shown to bind to heparins, the structural features of this interaction, the role of a plausible heparan sulfate proteoglycan (HSPG) receptor, and the antagonism of this pathway through small molecules remain unaddressed. Using an in vitro cellular assay, we demonstrate HSPGs modified by the 3-O-sulfotransferase isoform-3, but not isoform-5, preferentially increased SgP-mediated cell-to-cell fusion in comparison to control, unmodified, wild-type HSPGs. Computational studies support preferential recognition of the receptor-binding domain of SgP by 3-O-sulfated HS sequences. Competition with either fondaparinux, a 3-O-sulfated HS-binding oligopeptide, or a synthetic, non-sugar small molecule, blocked SgP-mediated cell-to-cell fusion. Finally, the synthetic, sulfated molecule inhibited fusion of GFP-tagged pseudo SARS-CoV-2 with human 293T cells with sub-micromolar potency. Overall, overexpression of 3-O-sulfated HSPGs contribute to fusion of SARS-CoV-2, which could be effectively antagonized by a synthetic, small molecule.
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Affiliation(s)
- Vaibhav Tiwari
- Department of Microbiology and Immunology, Midwestern University, Downers Grove, IL 60515
| | - Ritesh Tandon
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS 39216
| | - Nehru Viji Sankaranarayanan
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, 800 E. Leigh Street, Suite 212, Richmond, VA 23219
| | - Jacob C. Beer
- Department of Microbiology and Immunology, Midwestern University, Downers Grove, IL 60515
| | | | | | - Umesh R. Desai
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, 800 E. Leigh Street, Suite 212, Richmond, VA 23219
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Alabbas A, Desai UR. Enzyme immobilization offers a robust tool to scale up the production of longer, diverse, natural glycosaminoglycan oligosaccharides. Glycobiology 2020; 30:768-773. [PMID: 32193533 DOI: 10.1093/glycob/cwaa027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/15/2020] [Accepted: 03/18/2020] [Indexed: 11/14/2022] Open
Abstract
Although structurally diverse, longer glycosaminoglycan (GAG) oligosaccharides are critical to understand human biology, few are available. The major bottleneck has been the predominant production of oligosaccharides, primarily disaccharides, upon enzymatic depolymerization of GAGs. In this work, we employ enzyme immobilization to prepare hexasaccharide and longer sequences of chondroitin sulfate in good yields with reasonable homogeneity. Immobilized chondroitinase ABC displayed good efficiency, robust operational pH range, broad thermal stability, high recycle ability and excellent distribution of products in comparison to the free enzyme. Diverse sequences could be chromatographically resolved into well-defined peaks and characterized using LC-MS. Enzyme immobilization technology could enable easier access to diverse longer GAG sequences.
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Affiliation(s)
- Alhumaidi Alabbas
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA.,Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA.,Department of Pharmaceutical Chemistry, Prince Sattam Bin Abdulaziz University, Alkharj 11942, Saudi Arabia
| | - Umesh R Desai
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA.,Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
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Boothello RS, Sankaranarayanan NV, Afosah DK, Karuturi R, Al-Horani RA, Desai UR. Studies on fragment-based design of allosteric inhibitors of human factor XIa. Bioorg Med Chem 2020; 28:115762. [PMID: 32992249 DOI: 10.1016/j.bmc.2020.115762] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 08/24/2020] [Accepted: 09/06/2020] [Indexed: 12/16/2022]
Abstract
Human factor XIa (hFXIa) has emerged as an attractive target for development of new anticoagulants that promise higher level of safety. Different strategies have been adopted so far for the design of anti-hFXIa molecules including competitive and non-competitive inhibition. Of these, allosteric dysfunction of hFXIa's active site is especially promising because of the possibility of controlled reduction in activity that may offer a route to safer anticoagulants. In this work, we assess fragment-based design approach to realize a group of novel allosteric hFXIa inhibitors. Starting with our earlier discovery that sulfated quinazolinone (QAO) bind in the heparin-binding site of hFXIa, we developed a group of two dozen dimeric sulfated QAOs with intervening linkers that displayed a progressive variation in inhibition potency. In direct opposition to the traditional wisdom, increasing linker flexibility led to higher potency, which could be explained by computational studies. Sulfated QAO 19S was identified as the most potent and selective inhibitor of hFXIa. Enzyme inhibition studies revealed that 19S utilizes a non-competitive mechanism of action, which was supported by fluorescence studies showing a classic sigmoidal binding profile. Studies with selected mutants of hFXIa indicated that sulfated QAOs bind in heparin-binding site of the catalytic domain of hFXIa. Overall, the approach of fragment-based design offers considerable promise for designing heparin-binding site-directed allosteric inhibitors of hFXIa.
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Affiliation(s)
- Rio S Boothello
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, United States; Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, United States; Hunter Holmes McGuire Medical Center, Richmond, VA 23249, United States
| | - Nehru Viji Sankaranarayanan
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, United States; Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, United States
| | - Daniel K Afosah
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, United States; Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, United States
| | - Rajesh Karuturi
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, United States; Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, United States
| | - Rami A Al-Horani
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, United States; Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, United States; Division of Basic Pharmaceutical Sciences, College of Pharmacy, Xavier University of Louisiana, New Orleans, LA 70125, United States
| | - Umesh R Desai
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, United States; Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, United States.
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O'Hara CP, Boothello RS, Morla S, Vera A, Afosah DK, Sankaranarayanan NV, Nagarajan B, Sharon C, Patel BB, Desai UR. Abstract 6353: Cholesterol modification enhances potency and pharmacokinetic properties of a selective cancer stem cell targeting agent. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-6353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Increasing evidence supports the concept that tumor-initiating cancer stem cells (CSCs) are responsible for the relapse and reconstitution of formerly treated tumors. Previously, our lab identified a potent and selective inhibitor of colorectal CSCs, named G2.2, from a library of non-saccharide glycosaminoglycan mimetics (NSGMs). To further improve upon the potency, pharmacokinetics, and drug-like properties of G2.2, cholesterol-modified analogs were rationally designed using computational molecular modeling and molecular dynamics studies. A small group of designed NSGMs, labeled as G2C, G5C and G8C, were synthesized for biological evaluation. These agents and the parent NSGM G2.2 were studied for their ability to inhibit the growth of primary spheroids from a panel of 15 human colorectal cancer (CRC) cells representative of the consensus molecular subtypes of human CRC. Spheroid formation frequencies (SFFs) of cell lines were measured using limiting dilution assays (LDAs), and IC50 of inhibition was evaluated from dose-response curves for monolayer growth and primary spheroid growth in the presence of NSGMs. Selectivity of CSC targeting was assessed from the ratio of IC50,monolayer to IC50,spheroid. Pharmacokinetics (PK) and bioavailability in rodents were deduced following IV and PO administrations. In-vivo therapeutic potential of the NSGMs was studied in CSC-induced xenograft models aided by ex-vivo CSC phenotype characterization. Each NSGM preferentially targeted 3D spheroidal growth in comparison to monolayer cellular growth by 12- to 450-fold, suggesting excellent CSC selectivity. Cholesterol modification of G2.2 enhanced in-vitro spheroid inhibition potency across the entire panel of cell lines on average by 3- to 21-fold. G8C showed the highest inhibition potency with an IC50 of 1 to 10 μM across cell lines. Cells with higher SFF were several-fold more sensitive to NSGMs, suggesting that basal expression of CSCs could predict NSGM response. Robust reductions in tumor volumes were observed in mice treated with G5C (100 mg/kg i.p. 3x a week) following an intial-treatment with oxaliplatin and 5-fluorouracil (weekly x3) compared to vehicle controls. This reduction was concomitant with a 3.9-fold reduction in colonic crypt stemness marker LGR5+ cells and 2.6-fold decrease in xenograft-derived tertiary spheroids. No gross or organ specific toxicity was found in animals treated with G5C. Finally, cholesterol modification greatly improved PK and oral bioavailability of parent G2.2. Overall, cholesterol modification of CSC-selective G2.2 was found to enhance in vitro potency against spheroidal growth without compromising selectivity toward tumor initiating CSCs. The G2.2 analogs offered robust tumor reductions in vivo with essentially no off target toxicity, and serve as promising and novel potential cancer therapeutics.
Citation Format: Connor P. O'Hara, Rio S. Boothello, Shravan Morla, Alberto Vera, Daniel K. Afosah, Nehru V. Sankaranarayanan, Balaji Nagarajan, Chetna Sharon, Bhaumik B. Patel, Umesh R. Desai. Cholesterol modification enhances potency and pharmacokinetic properties of a selective cancer stem cell targeting agent [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6353.
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Morla S, Desai UR. Discovery of Sulfated Small Molecule Inhibitors of Matrix Metalloproteinase-8. Biomolecules 2020; 10:biom10081166. [PMID: 32784891 PMCID: PMC7465109 DOI: 10.3390/biom10081166] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 08/05/2020] [Accepted: 08/07/2020] [Indexed: 12/28/2022] Open
Abstract
Elevated matrix metalloproteinase-8 (MMP-8) activity contributes to the etiology of many diseases, including atherosclerosis, pulmonary fibrosis, and sepsis. Yet, very few small molecule inhibitors of MMP-8 have been identified. We reasoned that the synthetic non-sugar mimetics of glycosaminoglycans may inhibit MMP-8 because natural glycosaminoglycans are known to modulate the functions of various MMPs. The screening a library of 58 synthetic, sulfated mimetics consisting of a dozen scaffolds led to the identification of only two scaffolds, including sulfated benzofurans and sulfated quinazolinones, as promising inhibitors of MMP-8. Interestingly, the sulfated quinazolinones displayed full antagonism of MMP-8 and sulfated benzofuran appeared to show partial antagonism. Of the two, sulfated quinazolinones exhibited a >10-fold selectivity for MMP-8 over MMP-9, a closely related metalloproteinase. Molecular modeling suggested the plausible occupancy of the S1′ pocket on MMP-8 as the distinguishing feature of the interaction. Overall, this work provides the first proof that the sulfated mimetics of glycosaminoglycans could lead to potent, selective, and catalytic activity-tunable, small molecular inhibitors of MMP-8.
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Affiliation(s)
- Shravan Morla
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA;
- Drug Discovery and Development, Institute for Structural Biology, Virginia Commonwealth University, Richmond 23219, VA, USA
| | - Umesh R. Desai
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA;
- Drug Discovery and Development, Institute for Structural Biology, Virginia Commonwealth University, Richmond 23219, VA, USA
- Correspondence: ; Tel.: +804-828-7575; Fax: +804-827-3664
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Tiwari V, Beer JC, Sankaranarayanan NV, Swanson-Mungerson M, Desai UR. Discovering small-molecule therapeutics against SARS-CoV-2. Drug Discov Today 2020; 25:1535-1544. [PMID: 32574699 PMCID: PMC7305878 DOI: 10.1016/j.drudis.2020.06.017] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/19/2020] [Accepted: 06/16/2020] [Indexed: 02/08/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly become a global health pandemic. The lack of effective treatments, coupled with its etiology, has resulted in more than 400,000 deaths at the time of writing. The SARS-CoV-2 genome is highly homologous to that of SARS-CoV, the causative agent behind the 2003 SARS outbreak. Based on prior reports, clinicians have pursued the off-label use of several antiviral drugs, while the scientific community has responded by seeking agents against traditional targets, especially viral proteases. However, several avenues remain unexplored, including disrupting E and M protein oligomerization, outcompeting host glycan-virus interactions, interfering with the heparan sulfate proteoglycans-virus interaction, and others. In this review, we highlight some of these opportunities while summarizing the drugs currently in use against coronavirus 2019 (COVID-19).
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Affiliation(s)
- Vaibhav Tiwari
- Department of Microbiology and Immunology, College of Graduate Studies, Midwestern University Downers Grove, IL 6051, USA; Chicago College of Osteopathic Medicine, Midwestern University, Downers Grove, IL 60515, USA.
| | - Jacob C Beer
- Chicago College of Osteopathic Medicine, Midwestern University, Downers Grove, IL 60515, USA
| | - Nehru Viji Sankaranarayanan
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA; Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 2321, USA
| | - Michelle Swanson-Mungerson
- Department of Microbiology and Immunology, College of Graduate Studies, Midwestern University Downers Grove, IL 6051, USA; Chicago College of Osteopathic Medicine, Midwestern University, Downers Grove, IL 60515, USA
| | - Umesh R Desai
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA; Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 2321, USA.
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Nagarajan B, Sankaranarayanan NV, Desai UR. Rigorous analysis of free solution glycosaminoglycan dynamics using simple, new tools. Glycobiology 2020; 30:516-527. [PMID: 32080710 PMCID: PMC8179626 DOI: 10.1093/glycob/cwaa015] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 02/03/2020] [Accepted: 02/09/2020] [Indexed: 11/15/2022] Open
Abstract
Heparin/heparan sulfates (H/HS) are ubiquitous biopolymers that interact with many proteins to induce a range of biological functions. Unfortunately, how these biopolymers recognize their preferred protein targets remain poorly understood. It is suggested that computational simulations offer attractive avenues but a number of challenges, e.g., difficulty of selecting a comprehensive force field, few simple tools to interpret data, among others, remain. This work addresses several such challenges so as to help ease the implementation and analysis of computational experiments. First, this work presents a rigorous comparison of two different recent force fields, CHARMM36 and GLYCAM06, for H/HS studies. Second, it introduces two new straightforward parameters, i.e., end-to-end distance and minimum volume enclosing ellipsoid, to understand the myriad conformational forms of oligosaccharides that evolve over time in water. Third, it presents an application to elucidate the number and nature of inter and intramolecular, nondirect bridging water molecules, which help stabilize unique forms of H/HS. The results show that nonspecialists can use either CHARMM36 or GLYCAM06 force fields because both gave comparable results, albeit with small differences. The comparative study shows that the HS hexasaccharide samples a range of conformations with nearly equivalent energies, which could be the reason for its recognition by different proteins. Finally, analysis of the nondirect water bridges across the dynamics trajectory shows their importance in stabilization of certain conformational forms, which may become important for protein recognition. Overall, the work aids nonspecialists employ computational studies for understanding the solution behavior of H/HS.
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Affiliation(s)
- Balaji Nagarajan
- Institute for Structural Biology, Drug Discovery and Development, 800 E. Leigh Street, Suite 212, Richmond, VA 23219, USA
- Department of Medicinal Chemistry, 800 E. Leigh Street, Suite 205, Richmond, VA 23298, USA
| | - Nehru Viji Sankaranarayanan
- Institute for Structural Biology, Drug Discovery and Development, 800 E. Leigh Street, Suite 212, Richmond, VA 23219, USA
- Department of Medicinal Chemistry, 800 E. Leigh Street, Suite 205, Richmond, VA 23298, USA
| | - Umesh R Desai
- Institute for Structural Biology, Drug Discovery and Development, 800 E. Leigh Street, Suite 212, Richmond, VA 23219, USA
- Department of Medicinal Chemistry, 800 E. Leigh Street, Suite 205, Richmond, VA 23298, USA
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25
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Rajarathnam K, Desai UR. Structural Insights Into How Proteoglycans Determine Chemokine-CXCR1/CXCR2 Interactions: Progress and Challenges. Front Immunol 2020; 11:660. [PMID: 32391006 PMCID: PMC7193095 DOI: 10.3389/fimmu.2020.00660] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 03/23/2020] [Indexed: 01/01/2023] Open
Abstract
Proteoglycans (PGs), present in diverse environments, such as the cell membrane surface, extracellular milieu, and intracellular granules, are fundamental to life. Sulfated glycosaminoglycans (GAGs) are covalently attached to the core protein of proteoglycans. PGs are complex structures, and are diverse in terms of amino acid sequence, size, shape, and in the nature and number of attached GAG chains, and this diversity is further compounded by the phenomenal diversity in GAG structures. Chemokines play vital roles in human pathophysiology, from combating infection and cancer to leukocyte trafficking, immune surveillance, and neurobiology. Chemokines mediate their function by activating receptors that belong to the GPCR class, and receptor interactions are regulated by how, when, and where chemokines bind GAGs. GAGs fine-tune chemokine function by regulating monomer/dimer levels and chemotactic/haptotactic gradients, which are also coupled to how they are presented to their receptors. Despite their small size and similar structures, chemokines show a range of GAG-binding geometries, affinities, and specificities, indicating that chemokines have evolved to exploit the repertoire of chemical and structural features of GAGs. In this review, we summarize the current status of research on how GAG interactions regulate ELR-chemokine activation of CXCR1 and CXCR2 receptors, and discuss knowledge gaps that must be overcome to establish causal relationships governing the impact of GAG interactions on chemokine function in human health and disease.
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Affiliation(s)
- Krishna Rajarathnam
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX, United States.,Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch at Galveston, Galveston, TX, United States.,Department of Microbiology and Immunology, The University of Texas Medical Branch at Galveston, Galveston, TX, United States
| | - Umesh R Desai
- Department of Medicinal Chemistry, Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, United States
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Sankaranarayanan NV, Bi Y, Kuberan B, Desai UR. Combinatorial virtual library screening analysis of antithrombin binding oligosaccharide motif generation by heparan sulfate 3- O-Sulfotransferase 1. Comput Struct Biotechnol J 2020; 18:933-941. [PMID: 32346466 PMCID: PMC7183009 DOI: 10.1016/j.csbj.2020.03.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 03/07/2020] [Accepted: 03/08/2020] [Indexed: 12/31/2022] Open
Abstract
Pharmaceutical heparin's activity arises from a key high affinity and high selectivity antithrombin binding motif, which forms the basis for its use as an anticoagulant. The current problems with the supply of pig heparin raises the emphasis of understanding heparin biosynthesis so as to control and advance recombinantly expressed agent that could bypass the need for animals. Unfortunately, much remains to be understood about the generation of the antithrombin-binding motif by the key enzyme involved in its biosynthesis, 3-O-sulfotransferase-1 (3OST-1). In this work, we present a novel computational approach to understand recognition of oligosaccharide sequences by 3OST-1. Application of combinatorial virtual library screening (CVLS) algorithm on hundreds of tetrasaccharide and hexasaccharide sequences shows that 3OST-1 belongs to the growing number of proteins that recognize glycosaminoglycans with very high selectivity. It prefers very well defined pentasaccharide sequences carrying distinct groups in each of the five residues to generate the antithrombin binding motif. CVLS also identifies key residues including His271, Arg72, Arg197 and Lys173, which interact with 6-sulfate, 5-COO¯, 2-/6-sulfates and 2-sulfate at the -2, -1, +2, and +1 positions of the precursor pentasaccharide, respectively. Additionally, uncharged residues, especially Gln163 and Asn167, were also identified as playing important roles in recognition. Overall, the success of CVLS in predicting 3OST-1 recognition characteristics that help engineer selectivity lead to the expectation that recombinant enzymes could be designed to help resolve the current problems in the supply of anticoagulant heparin.
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Affiliation(s)
- Nehru Viji Sankaranarayanan
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, United States
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, United States
| | - Yiling Bi
- Departments of Biology, Bioengineering & Medicinal Chemistry and Interdepartmental Program in Neurosciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Balagurunathan Kuberan
- Departments of Biology, Bioengineering & Medicinal Chemistry and Interdepartmental Program in Neurosciences, University of Utah, Salt Lake City, UT 84112, USA
- Interdepartmental Program in Neurosciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Umesh R. Desai
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, United States
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, United States
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27
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Desai UR. A Tool to Predict Affinity and Specificity of GAG Binding to Proteins. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.01998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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28
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Elste J, Kaltenbach D, Patel VR, Nguyen MT, Sharthiya H, Tandon R, Mehta SK, Volin MV, Fornaro M, Tiwari V, Desai UR. Inhibition of Human Cytomegalovirus Entry into Host Cells Through a Pleiotropic Small Molecule. Int J Mol Sci 2020; 21:ijms21051676. [PMID: 32121406 PMCID: PMC7084493 DOI: 10.3390/ijms21051676] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/19/2020] [Accepted: 02/26/2020] [Indexed: 12/11/2022] Open
Abstract
Human cytomegalovirus (HCMV) infections are wide-spread among the general population with manifestations ranging from asymptomatic to severe developmental disabilities in newborns and life-threatening illnesses in individuals with a compromised immune system. Nearly all current drugs suffer from one or more limitations, which emphasizes the critical need to develop new approaches and new molecules. We reasoned that a ‘poly-pharmacy’ approach relying on simultaneous binding to multiple receptors involved in HCMV entry into host cells could pave the way to a more effective therapeutic outcome. This work presents the study of a synthetic, small molecule displaying pleiotropicity of interactions as a competitive antagonist of viral or cell surface receptors including heparan sulfate proteoglycans and heparan sulfate-binding proteins, which play important roles in HCMV entry and spread. Sulfated pentagalloylglucoside (SPGG), a functional mimetic of heparan sulfate, inhibits HCMV entry into human foreskin fibroblasts and neuroepithelioma cells with high potency. At the same time, SPGG exhibits no toxicity at levels as high as 50-fold more than its inhibition potency. Interestingly, cell-ELISA assays showed downregulation in HCMV immediate-early gene 1 and 2 (IE 1&2) expression in presence of SPGG further supporting inhibition of viral entry. Finally, HCMV foci were observed to decrease significantly in the presence of SPGG suggesting impact on viral spread too. Overall, this work offers the first evidence that pleiotropicity, such as demonstrated by SPGG, may offer a new poly-therapeutic approach toward effective inhibition of HCMV.
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Affiliation(s)
- James Elste
- Department of Microbiology & Immunology, College of Graduate Studies and Chicago College of Osteopathic Medicine, Midwestern University, Downers Grove, IL 60515, USA; (J.E.); (V.R.P.); (M.T.N.); (M.V.V.)
| | - Dominik Kaltenbach
- Department of Biomedical Sciences, College of Graduate Studies, Midwestern University, Downers Grove, IL 60515, USA;
| | - Vraj R. Patel
- Department of Microbiology & Immunology, College of Graduate Studies and Chicago College of Osteopathic Medicine, Midwestern University, Downers Grove, IL 60515, USA; (J.E.); (V.R.P.); (M.T.N.); (M.V.V.)
| | - Max T. Nguyen
- Department of Microbiology & Immunology, College of Graduate Studies and Chicago College of Osteopathic Medicine, Midwestern University, Downers Grove, IL 60515, USA; (J.E.); (V.R.P.); (M.T.N.); (M.V.V.)
| | - Harsh Sharthiya
- Department of Anatomy, College of Graduate Studies and Chicago College of Osteopathic Medicine, Midwestern University, Downers Grove, IL 60515, USA; (H.S.); (M.F.)
| | - Ritesh Tandon
- Department of Microbiology and Immunology, University of Mississippi Medical Center, 2500 North State Street, Jackson, MS 39216, USA;
| | | | - Michael V. Volin
- Department of Microbiology & Immunology, College of Graduate Studies and Chicago College of Osteopathic Medicine, Midwestern University, Downers Grove, IL 60515, USA; (J.E.); (V.R.P.); (M.T.N.); (M.V.V.)
| | - Michele Fornaro
- Department of Anatomy, College of Graduate Studies and Chicago College of Osteopathic Medicine, Midwestern University, Downers Grove, IL 60515, USA; (H.S.); (M.F.)
| | - Vaibhav Tiwari
- Department of Microbiology & Immunology, College of Graduate Studies and Chicago College of Osteopathic Medicine, Midwestern University, Downers Grove, IL 60515, USA; (J.E.); (V.R.P.); (M.T.N.); (M.V.V.)
- Correspondence: (V.T.); (U.R.D.)
| | - Umesh R. Desai
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA
- Correspondence: (V.T.); (U.R.D.)
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29
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Kalita M, Chua JS, Boothello RS, Joice A, Antelope O, Roy A, Anandh Babu PV, Saijoh Y, Desai UR, Kuberan B. Visualizing antithrombin-binding 3-O-sulfated heparan sulfate motifs on cell surfaces. Chem Commun (Camb) 2020; 56:14423-14426. [DOI: 10.1039/d0cc05893a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
To map the cellular topography of the rare 3-O-sulfated structural motif of heparan sulfate (HS), we constructed quantum dot-based probes for antithrombin and FGF2, which reveal widely different distribution of the targeted HS motifs.
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Affiliation(s)
- Mausam Kalita
- Departments of Medicinal Chemistry and Bioengineering
- University of Utah
- Salt Lake City
- USA
| | - Jie Shi Chua
- Departments of Medicinal Chemistry and Bioengineering
- University of Utah
- Salt Lake City
- USA
| | - Rio S. Boothello
- Department of Medicinal Chemistry
- School of Pharmacy
- Virginia Commonwealth University
- Richmond
- USA
| | - April Joice
- Departments of Medicinal Chemistry and Bioengineering
- University of Utah
- Salt Lake City
- USA
| | - Orlando Antelope
- Departments of Medicinal Chemistry and Bioengineering
- University of Utah
- Salt Lake City
- USA
| | - Anindita Roy
- Departments of Medicinal Chemistry and Bioengineering
- University of Utah
- Salt Lake City
- USA
| | | | - Yukio Saijoh
- Department of Neurobiology and Anatomy, University of Utah School of Medicine
- Salt Lake City
- USA
| | - Umesh R. Desai
- Department of Medicinal Chemistry
- School of Pharmacy
- Virginia Commonwealth University
- Richmond
- USA
| | - Balagurunathan Kuberan
- Departments of Medicinal Chemistry and Bioengineering
- University of Utah
- Salt Lake City
- USA
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30
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Al-Horani RA, Abdelfadiel EI, Afosah DK, Morla S, Sistla JC, Mohammed B, Martin EJ, Sakagami M, Brophy DF, Desai UR. A synthetic heparin mimetic that allosterically inhibits factor XIa and reduces thrombosis in vivo without enhanced risk of bleeding. J Thromb Haemost 2019; 17:2110-2122. [PMID: 31397071 PMCID: PMC6893084 DOI: 10.1111/jth.14606] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 07/15/2019] [Accepted: 08/07/2019] [Indexed: 12/14/2022]
Abstract
BACKGROUND Human factor XIa (FXIa) is an actively pursued target for development of safer anticoagulants. Our long-standing hypothesis has been that allosterism originating from heparin-binding site(s) on coagulation enzymes is a promising approach to yield safer agents. OBJECTIVES To develop a synthetic heparin mimetic as an inhibitor of FXIa so as to reduce clot formation in vivo but not carry high bleeding risk. METHODS We employed a gamut of methods involving synthetic chemistry, biophysical biochemistry, enzyme assays, blood and plasma coagulation assays, and in vivo thrombosis models in this work. RESULTS Sulfated chiro-inositol (SCI), a non-saccharide mimetic of heparin, was synthesized in three steps in overall yields of >50%. SCI inhibited FXIa with potency of 280 nmol/L and preferentially engaged FXIa's heparin-binding site to conformationally alter its active site. SCI inhibition of FXIa could be rapidly reversed by common antidotes, such as protamine. SCI preferentially prolonged plasma clotting initiated with recalcification, rather than thromboplastin, alluding to its intrinsic pathway-based mechanism. Human blood thromboelastography indicated good ex vivo anticoagulation properties of SCI. Rat tail bleeding and maximum-dose-tolerated studies indicated that no major bleeding or toxicity concerns for SCI suggesting a potentially safer anticoagulation outcome. FeCl3 -induced arterial and thromboplastin-induced venous thrombosis model studies in the rat showed reduced thrombus formation by SCI at 250 μg/animal, which matched enoxaparin at 2500 μg/animal. CONCLUSIONS Overall, SCI is a highly promising, allosteric inhibitor of FXIa that induces potent anticoagulation in vivo. Further studies are necessary to assess SCI in animal models mimicking human clinical indications.
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Affiliation(s)
- Rami A. Al-Horani
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219
| | - Elsamani I. Abdelfadiel
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219
- Department of Biochemistry, Virginia Commonwealth University, Richmond, VA 23298
| | - Daniel K. Afosah
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219
| | - Shravan Morla
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219
| | - Jyothi C. Sistla
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219
| | - Bassem Mohammed
- Department of Pharmacotherapy and Outcomes Sciences, Virginia Commonwealth University, Richmond, VA 23298
| | - Erika J. Martin
- Department of Pharmacotherapy and Outcomes Sciences, Virginia Commonwealth University, Richmond, VA 23298
| | - Masahiro Sakagami
- Department of Pharmaceutics, Virginia Commonwealth University, Richmond, VA 23298
| | - Donald F. Brophy
- Department of Pharmacotherapy and Outcomes Sciences, Virginia Commonwealth University, Richmond, VA 23298
| | - Umesh R. Desai
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219
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Abstract
Heparanase, an endo-β-D-glucuronidase, cleaves cell surface and extracellular matrix heparan sulfate (HS) chains at distinct sites and plays important biological roles including modulation of cell growth and metastasis. Although a number of different types of heparanase assays have been reported to date, most are labor intensive, complex and/or expensive to carry out. We reasoned that a simpler heparanase assay could be developed using heparin labeled with Dabcyl and EDANS as donor and acceptor fluorophores so as to generate a FRET signal. Our results show that a more robust heparanase assay could be developed based on the principle studied herein and more homogeneous preparation of heparin. Yet, the assay in its current form could be used for routine screening of potential inhibitors in a high-throughput manner as well as for studying heparanase activity expressed in tumors as well as biological fluids like plasma.
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Affiliation(s)
- Jyothi C Sistla
- Institute for Structural Biology, Drug Discovery, and Development, Virginia Commonwealth University, Richmond, VA 23219, USA.,Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Umesh R Desai
- Institute for Structural Biology, Drug Discovery, and Development, Virginia Commonwealth University, Richmond, VA 23219, USA.,Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA
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32
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Morla S, Sankaranarayanan NV, Afosah DK, Kumar M, Kummarapurugu AB, Voynow JA, Desai UR. On the Process of Discovering Leads That Target the Heparin-Binding Site of Neutrophil Elastase in the Sputum of Cystic Fibrosis Patients. J Med Chem 2019; 62:5501-5511. [PMID: 31074986 DOI: 10.1021/acs.jmedchem.9b00379] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cystic fibrosis (CF) is a disease of dysregulated salt and fluid homeostasis that results in the massive accumulation of neutrophil elastase, resulting in lung degradation and death. The current CF therapy relies on inhaled deoxyribonuclease and hypertonic saline but does not address the elastolytic degradation of the lung. We reasoned that allosteric agents targeting the heparin-binding site of neutrophil elastase would offer a therapeutic paradigm. Screening a library of 60 nonsaccharide glycosaminoglycan mimetics (NSGMs) led to the discovery of 23 hits against neutrophil elastase. To identify a lead NSGM that works in sync with the current CF-relieving agents, we developed a rigorous protocol based on fundamental computational, biochemical, mechanistic, and adverse effect studies. The lead NSGM so identified neutralized neutrophil elastase present in the sputum of CF patients in the presence of deoxyribonuclease and high-salt conditions. Our work presents the process for discovering potent, small, synthetic, allosteric, anti-CF agents, while also identifying a novel lead for further studies in animal models of CF.
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Affiliation(s)
- Shravan Morla
- Department of Medicinal Chemistry , Virginia Commonwealth University , Richmond , Virginia 23298 , United States.,Institute for Structural Biology, Drug Discovery and Development , Virginia Commonwealth University , Richmond , Virginia 23219 , United States
| | - Nehru Viji Sankaranarayanan
- Department of Medicinal Chemistry , Virginia Commonwealth University , Richmond , Virginia 23298 , United States.,Institute for Structural Biology, Drug Discovery and Development , Virginia Commonwealth University , Richmond , Virginia 23219 , United States
| | - Daniel K Afosah
- Department of Medicinal Chemistry , Virginia Commonwealth University , Richmond , Virginia 23298 , United States.,Institute for Structural Biology, Drug Discovery and Development , Virginia Commonwealth University , Richmond , Virginia 23219 , United States
| | - Megh Kumar
- Department of Medicinal Chemistry , Virginia Commonwealth University , Richmond , Virginia 23298 , United States.,Institute for Structural Biology, Drug Discovery and Development , Virginia Commonwealth University , Richmond , Virginia 23219 , United States
| | - Apparao B Kummarapurugu
- Children's Hospital of Richmond at Virginia Commonwealth University , Richmond , Virginia 23298 , United States
| | - Judith A Voynow
- Children's Hospital of Richmond at Virginia Commonwealth University , Richmond , Virginia 23298 , United States
| | - Umesh R Desai
- Department of Medicinal Chemistry , Virginia Commonwealth University , Richmond , Virginia 23298 , United States.,Institute for Structural Biology, Drug Discovery and Development , Virginia Commonwealth University , Richmond , Virginia 23219 , United States
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33
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Ongolu RK, Afosah D, Sistla J, Hawkridge A, Desai UR. Design and Synthesis of Photoaffinity Probe for Identification of Protein Targets of Glycosaminoglycan Mimetics. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.784.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ravi Kumar Ongolu
- Medicinal ChemistryVirginia Commonwealth UniversityRichmondVA
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth UniversityRichmondVA
| | - Daniel Afosah
- Medicinal ChemistryVirginia Commonwealth UniversityRichmondVA
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth UniversityRichmondVA
| | - Jyothi Sistla
- Medicinal ChemistryVirginia Commonwealth UniversityRichmondVA
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth UniversityRichmondVA
| | - Adam Hawkridge
- PharmaceuticsVirginia Commonwealth UniversityRichmondVA
- Pharmacotherapy and Outcomes SciencesVirginia Commonwealth UniversityRichmondVA
| | - Umesh R. Desai
- Medicinal ChemistryVirginia Commonwealth UniversityRichmondVA
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth UniversityRichmondVA
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34
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Sistla JC, Afosah DK, Morla S, Patel NJ, Patel BB, Desai UR. A small, synthetic glycosaminoglycan mimetic as an inhibitor of human heparanase. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.675.12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jyothi C. Sistla
- Department of Medicinal ChemistryVirginia Commonwealth UniversityRichmondVA
- Institute for Structural BiologyDrug Discovery and DevelopmentRichmondVA
| | - Daniel K Afosah
- Department of Medicinal ChemistryVirginia Commonwealth UniversityRichmondVA
- Institute for Structural BiologyDrug Discovery and DevelopmentRichmondVA
| | - Shravan Morla
- Department of Medicinal ChemistryVirginia Commonwealth UniversityRichmondVA
- Institute for Structural BiologyDrug Discovery and DevelopmentRichmondVA
| | | | - Bhaumik B. Patel
- Division of Hematology, Oncology, and Palliative Care, Department of Internal Medicine and Massey Cancer CenterVirginia Commonwealth UniversityRichmondVA
- Hunter Holmes McGuire VA Medical CenterRichmondVA
| | - Umesh R. Desai
- Department of Medicinal ChemistryVirginia Commonwealth UniversityRichmondVA
- Institute for Structural BiologyDrug Discovery and DevelopmentRichmondVA
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35
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Nagarajan B, Sepuru KM, Rajarathnam K, Desai UR. Glycosaminoglycan Recognition of Neutrophil‐Activating Chemokines. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.800.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Balaji Nagarajan
- Department of Medicinal ChemistryInstitute for Structural Biology, Drug Discovery and DevelopmentRichmondVA
| | | | - Krishna Rajarathnam
- Department of Biochemistry & Molecular BiologyGalvestonTX
- Sealy Center for Structural Biology and Molecular BiophysicsGalvestonTX
| | - Umesh R Desai
- Department of Medicinal ChemistryInstitute for Structural Biology, Drug Discovery and DevelopmentRichmondVA
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36
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Sankaranarayanan NV, Desai UR. Towards computational prediction of the heparan sulfate interactome. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.800.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Nehru Viji Sankaranarayanan
- Department of Medicinal ChemistryInstitute for Structural Biology, Drug Discovery, and Development; Virginia Commonwealth UniversityRichmondVA
| | - Umesh R Desai
- Department of Medicinal ChemistryInstitute for Structural Biology, Drug Discovery, and Development; Virginia Commonwealth UniversityRichmondVA
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37
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Morla S, Afosah DK, O'Hara C, Boothello R, Patel BB, Sakagami M, Desai UR. Lipophilic Modification of an Anti‐Cancer Stem Cell Agent Improves Pharmacokinetic and Anti‐Cancer Properties. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.782.17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Shravan Morla
- Medicinal ChemistryVirginia Commonwealth UniveristyRichmondVA
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth UniveristyRichmondVA
| | - Daniel K. Afosah
- Medicinal ChemistryVirginia Commonwealth UniveristyRichmondVA
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth UniveristyRichmondVA
| | - Connor O'Hara
- Medicinal ChemistryVirginia Commonwealth UniveristyRichmondVA
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth UniveristyRichmondVA
| | - Rio Boothello
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth UniveristyRichmondVA
| | | | | | - Umesh R. Desai
- Medicinal ChemistryVirginia Commonwealth UniveristyRichmondVA
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth UniveristyRichmondVA
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38
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Nagarajan B, Sankaranarayanan NV, Desai UR. Perspective on computational simulations of glycosaminoglycans. Wiley Interdiscip Rev Comput Mol Sci 2019; 9:e1388. [PMID: 31080520 PMCID: PMC6504973 DOI: 10.1002/wcms.1388] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/07/2018] [Indexed: 01/06/2023]
Abstract
Glycosaminoglycans (GAGs) represent a formidable frontier for chemists, biochemists, biologists, medicinal chemists and drug delivery specialists because of massive structural complexity. GAGs are arguably the most complex, natural linear biopolymers with theoretical diversity orders of magnitude higher than proteins and nucleic acids. Yet, this diversity remains generally untapped. Computational approaches offer major routes to understand GAG structure and dynamics so as to enable novel applications of these biopolymers. In fact, computational algorithms, softwares, online tools and techniques have reached a level of sophistication that help understand atomistic details of conformational variation and protein recognition of individual GAG sequences. This review describes current approaches and challenges in computational study of GAGs. It presents a history of major findings since the earliest mention of GAGs (the 1960s), the development of parameters and force fields specific for GAGs, and the application of these tools in understanding GAG structure-function relationship. This review also presents a section on how to perform simulation of GAGs, which is directed toward researchers interested in entering this promising field with potential to impact therapy.
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Affiliation(s)
- Balaji Nagarajan
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond,
VA 23298, USA
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Nehru Viji Sankaranarayanan
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond,
VA 23298, USA
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Umesh R. Desai
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond,
VA 23298, USA
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
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39
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Patel NR, Patel DV, Kanhed AM, Patel SP, Patel KV, Afosah DK, Desai UR, Karpoormath R, Yadav MR. 2-Aminobenzamide-Based Factor Xa Inhibitors with Novel Mono- and Bi-Aryls as S4 Binding Elements. ChemistrySelect 2019. [DOI: 10.1002/slct.201803342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Nirav R. Patel
- Faculty of Pharmacy; Kalabhavan Campus; The Maharaja Sayajirao University of Baroda, Vadodara-; 390001 Gujarat India
| | - Dushyant V. Patel
- Faculty of Pharmacy; Kalabhavan Campus; The Maharaja Sayajirao University of Baroda, Vadodara-; 390001 Gujarat India
| | - Ashish M. Kanhed
- Faculty of Pharmacy; Kalabhavan Campus; The Maharaja Sayajirao University of Baroda, Vadodara-; 390001 Gujarat India
- Department of Pharmaceutical Chemistry; Discipline of Pharmaceutical Sciences; College of Health Sciences; University of KwaZulu-Natal (Westville); Durban 4000 South Africa
| | - Sagar P. Patel
- Faculty of Pharmacy; Kalabhavan Campus; The Maharaja Sayajirao University of Baroda, Vadodara-; 390001 Gujarat India
| | - Kirti V. Patel
- Faculty of Pharmacy; Kalabhavan Campus; The Maharaja Sayajirao University of Baroda, Vadodara-; 390001 Gujarat India
| | - Daniel K. Afosah
- Department of Medicinal Chemistry and Institute for Structrural Biology and Drug Discovery; Virginia Commonwealth University, Richmond; Virginia 23219 United States
| | - Umesh R. Desai
- Department of Medicinal Chemistry and Institute for Structrural Biology and Drug Discovery; Virginia Commonwealth University, Richmond; Virginia 23219 United States
| | - Rajshekhar Karpoormath
- Department of Pharmaceutical Chemistry; Discipline of Pharmaceutical Sciences; College of Health Sciences; University of KwaZulu-Natal (Westville); Durban 4000 South Africa
| | - Mange Ram Yadav
- Faculty of Pharmacy; Kalabhavan Campus; The Maharaja Sayajirao University of Baroda, Vadodara-; 390001 Gujarat India
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Gallegos KM, Taylor CR, Rabulinski DJ, Del Toro R, Girgis DE, Jourha D, Tiwari V, Desai UR, Ramsey KH. A Synthetic, Small, Sulfated Agent Is a Promising Inhibitor of Chlamydia spp. Infection in vivo. Front Microbiol 2019; 9:3269. [PMID: 30700982 PMCID: PMC6343517 DOI: 10.3389/fmicb.2018.03269] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 12/17/2018] [Indexed: 01/19/2023] Open
Abstract
Chlamydia is the most frequently reported sexually transmitted bacteria causing 2.9 million infections annually in the United States. Diagnosis, treatment, and sequelae of chlamydial disease cost billions of dollars each year in the United States alone. Considering that a heparin sulfate-like cell surface receptor is involved in Chlamydia infections, we reasoned that sulfated and sulfonated mimics of heparin sulfate would be useful in topical prophylactic prevention of Chlamydia. In this study, we tested a small, synthetic sulfated agent sulfated pentagalloyl glucoside (SPGG) and three synthetic sulfonated polymers PSS and SPS with average molecular weight in the range of 11 to 1000 kDa for inhibition against Chlamydia. Infection of HeLa cells with C. muridarum or C. trachomatis in the presence of increasing concentrations of SPGG or sulfonated polymers were quantified by immunofluorescence of Chlamydia inclusions. To determine whether in vitro pre-treatment of SPGG inhibits infection of C. muridarum, HeLa monolayers were incubated with SPGG-containing media, and then infected with Chlamydia. Our in vitro results show that SPGG pre-treatment inhibits Chlamydia infection in a dose-dependent manner. In addition, we further determined if SPGG treatment has an inhibitory effect during infection, therefore cell monolayers were infected with C. muridarum in the concurrent presence of SPGG. Our results show that SPGG inhibits C. muridarum infection with an IC50 at 10 μg/ml levels. We also tested the inhibitory effect of synthetic polymers PSS and SPS against Chlamydia and found inhibition of C. muridarum and C. trachomatis infections with IC50 ranging from 0.3 to 0.8 μg/ml. SPGG, PSS, and SPS inhibit formation of Chlamydia inclusions in a concentration-dependent manner. For evaluation of in vivo efficacy of the most effective agent in blocking C. muridarum, SPGG, we intravaginally pre-treated mice with SPGG before infection with C. muridarum. Cervical swabs were collected post-infection to quantify Chlamydia inclusions in vitro. Our in vivo data show that the SPGG-treated group has a statistically significant reduction of infection compared to the no-treatment control. Overall, our results show that SPGG could serve as a promising topical inhibitor for preventing Chlamydia infection.
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Affiliation(s)
- Karen M. Gallegos
- Department of Microbiology and Immunology, College of Graduate Studies, Midwestern University, Downers Grove, IL, United States
| | - Christopher R. Taylor
- Department of Microbiology and Immunology, College of Graduate Studies, Midwestern University, Downers Grove, IL, United States
- Department of Dermatology, Charles C. Gates Center for Regenerative Medicine and Stem Cell Biology, University of Colorado – Anschutz Medical Campus, Aurora, CO, United States
| | - Daniel J. Rabulinski
- Department of Microbiology and Immunology, College of Graduate Studies, Midwestern University, Downers Grove, IL, United States
| | - Rosalinda Del Toro
- Department of Microbiology and Immunology, College of Graduate Studies, Midwestern University, Downers Grove, IL, United States
| | - Danielle E. Girgis
- Department of Microbiology and Immunology, College of Graduate Studies, Midwestern University, Downers Grove, IL, United States
| | - Dapinder Jourha
- Department of Microbiology and Immunology, College of Graduate Studies, Midwestern University, Downers Grove, IL, United States
| | - Vaibhav Tiwari
- Department of Microbiology and Immunology, College of Graduate Studies, Midwestern University, Downers Grove, IL, United States
| | - Umesh R. Desai
- Institute for Structural Biology, Drug Discovery and Development, Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA, United States
| | - Kyle H. Ramsey
- Department of Microbiology and Immunology, College of Graduate Studies, Midwestern University, Downers Grove, IL, United States
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Boothello RS, Patel NJ, Sharon C, Abdelfadiel EI, Morla S, Brophy DF, Lippman HR, Desai UR, Patel BB. A Unique Nonsaccharide Mimetic of Heparin Hexasaccharide Inhibits Colon Cancer Stem Cells via p38 MAP Kinase Activation. Mol Cancer Ther 2019; 18:51-61. [PMID: 30337351 PMCID: PMC6332501 DOI: 10.1158/1535-7163.mct-18-0104] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 07/23/2018] [Accepted: 10/12/2018] [Indexed: 12/13/2022]
Abstract
Targeting of cancer stem cells (CSC) is expected to be a paradigm-shifting approach for the treatment of cancers. Cell surface proteoglycans bearing sulfated glycosaminoglycan (GAG) chains are known to play a critical role in the regulation of stem cell fate. Here, we show for the first time that G2.2, a sulfated nonsaccharide GAG mimetic (NSGM) of heparin hexasaccharide, selectively inhibits colonic CSCs in vivo G2.2-reduced CSCs (CD133+/CXCR4+, Dual hi) induced HT-29 and HCT 116 colon xenografts' growth in a dose-dependent fashion. G2.2 also significantly delayed the growth of colon xenograft further enriched in CSCs following oxaliplatin and 5-fluorouracil treatment compared with vehicle-treated xenograft controls. In fact, G2.2 robustly inhibited CSCs' abundance (measured by levels of CSC markers, e.g., CD133, DCMLK1, LGR5, and LRIG1) and self-renewal (quaternary spheroids) in colon cancer xenografts. Intriguingly, G2.2 selectively induced apoptosis in the Dual hi CSCs in vivo eluding to its CSC targeting effects. More importantly, G2.2 displayed none to minimal toxicity as observed through morphologic and biochemical studies of vital organ functions, blood coagulation profile, and ex vivo analyses of normal intestinal (and bone marrow) progenitor cell growth. Through extensive in vitro, in vivo, and ex vivo mechanistic studies, we showed that G2.2's inhibition of CSC self-renewal was mediated through activation of p38α, uncovering important signaling that can be targeted to deplete CSCs selectively while minimizing host toxicity. Hence, G2.2 represents a first-in-class (NSGM) anticancer agent to reduce colorectal CSCs.
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Affiliation(s)
- Rio S Boothello
- Division of Hematology and Oncology, Department of Internal Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia
- McGuire VA Medical Center, Richmond, Virginia
| | - Nirmita J Patel
- McGuire VA Medical Center, Richmond, Virginia
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia
| | | | - Elsamani I Abdelfadiel
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia
| | - Shravan Morla
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia
| | - Donald F Brophy
- Department of Pharmacotherapy and Outcomes Sciences, Virginia Commonwealth University, Richmond, Virginia
| | | | - Umesh R Desai
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia.
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia
| | - Bhaumik B Patel
- Division of Hematology and Oncology, Department of Internal Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia.
- McGuire VA Medical Center, Richmond, Virginia
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42
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Majmudar H, Hao M, Sankaranarayanan NV, Zanotti B, Volin MV, Desai UR, Tiwari V. A synthetic glycosaminoglycan mimetic blocks HSV-1 infection in human iris stromal cells. Antiviral Res 2018; 161:154-162. [PMID: 30481525 DOI: 10.1016/j.antiviral.2018.11.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 11/09/2018] [Accepted: 11/15/2018] [Indexed: 11/26/2022]
Abstract
Herpes simplex virus type-1 (HSV-1) is a significant pathogen that affects vision by targeting multiple regions in the human eye including iris. Using a focused library of synthetic non-saccharide glycosaminoglycan mimetics (NSGMs), we identified sulfated pentagalloylglucoside (SPGG) as a potent inhibitor of HSV-1 entry and cell-to-cell spread in the primary cultures of human iris stromal (HIS) cells isolated from eye donors. Using in vitro β-galactosidase reporter assay and plaque reduction assay, SPGG was found to inhibit HSV-1 entry in a dosage-dependent manner (IC50 ∼6.0 μM). Interestingly, a pronounced inhibition in HSV-1 entry and spread was observed in HIS cells, or a cell line expressing specific gD-receptor, when virions were pre-treated with mimetics suggesting a possible interaction between SPGG and the HSV-1 glycoprotein. To examine the significance of gD-SPGG interaction, HIS cells were pretreated with SPGG, which showed a significant reduction in gD binding. Taken together, our results provide strong evidence of SPGG being a novel viral entry inhibitor against ocular HSV infection.
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Affiliation(s)
- Hardik Majmudar
- Department of Microbiology & Immunology, College of Graduate Studies, Midwestern University, Downers Grove, IL 60515, USA
| | - Meng Hao
- Department of Microbiology & Immunology, College of Graduate Studies, Midwestern University, Downers Grove, IL 60515, USA
| | - Nehru Viji Sankaranarayanan
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Brian Zanotti
- Department of Microbiology & Immunology, College of Graduate Studies, Midwestern University, Downers Grove, IL 60515, USA
| | - Michael V Volin
- Department of Microbiology & Immunology, College of Graduate Studies, Midwestern University, Downers Grove, IL 60515, USA
| | - Umesh R Desai
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Vaibhav Tiwari
- Department of Microbiology & Immunology, College of Graduate Studies, Midwestern University, Downers Grove, IL 60515, USA.
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43
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Kaltenbach DD, Jaishankar D, Hao M, Beer JC, Volin MV, Desai UR, Tiwari V. Sulfotransferase and Heparanase: Remodeling Engines in Promoting Virus Infection and Disease Development. Front Pharmacol 2018; 9:1315. [PMID: 30555321 PMCID: PMC6282075 DOI: 10.3389/fphar.2018.01315] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 10/29/2018] [Indexed: 01/08/2023] Open
Abstract
An extraordinary binding site generated in heparan sulfate (HS) structures, during its biosynthesis, provides a unique opportunity to interact with multiple protein ligands including viral proteins, and therefore adds tremendous value to this master molecule. An example of such a moiety is the sulfation at the C3 position of glucosamine residues in HS chain via 3-O sulfotransferase (3-OST) enzymes, which generates a unique virus-cell fusion receptor during herpes simplex virus (HSV) entry and spread. Emerging evidence now suggests that the unique patterns in HS sulfation assist multiple viruses in invading host cells at various steps of their life cycles. In addition, sulfated-HS structures are known to assist in invading host defense mechanisms and initiating multiple inflammatory processes; a critical event in the disease development. All these processes are detrimental for the host and therefore raise the question of how HS-sulfation is regulated. Epigenetic modulations have been shown to be implicated in these reactions during HSV infection as well as in HS modifying enzyme sulfotransferases, and therefore pose a critical component in answering it. Interestingly, heparanase (HPSE) activity is shown to be upregulated during virus infection and multiple other diseases assisting in virus replication to promote cell and tissue damage. These phenomena suggest that sulfotransferases and HPSE serve as key players in extracellular matrix remodeling and possibly generating unique signatures in a given disease. Therefore, identifying the epigenetic regulation of OST genes, and HPSE resulting in altered yet specific sulfation patterns in HS chain during virus infection, will be a significant a step toward developing potential diagnostic markers and designing novel therapies.
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Affiliation(s)
- Dominik D Kaltenbach
- Department of Biomedical Sciences, College of Graduate Studies, Midwestern University, Downers Grove, IL, United States
| | - Dinesh Jaishankar
- Department of Ophthalmology & Visual Sciences, University of Illinois at Chicago, Chicago, IL, United States
| | - Meng Hao
- Chicago College of Pharmacy, Midwestern University, Downers Grove, IL, United States
| | - Jacob C Beer
- Chicago College of Osteopathic Medicine, Midwestern University, Downers Grove, IL, United States
| | - Michael V Volin
- Department of Microbiology & Immunology, College of Graduate Studies, Midwestern University, Downers Grove, IL, United States
| | - Umesh R Desai
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, United States
| | - Vaibhav Tiwari
- Department of Microbiology & Immunology, College of Graduate Studies, Midwestern University, Downers Grove, IL, United States
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44
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Sistla JC, Morla S, Alabbas AHB, Kalathur RC, Sharon C, Patel BB, Desai UR. Polymeric fluorescent heparin as one-step FRET substrate of human heparanase. Carbohydr Polym 2018; 205:385-391. [PMID: 30446119 DOI: 10.1016/j.carbpol.2018.10.071] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 09/29/2018] [Accepted: 10/22/2018] [Indexed: 01/21/2023]
Abstract
Heparanase, an endo-β-D-glucuronidase, cleaves cell surface and extracellular matrix heparan sulfate (HS) chains and plays important roles in cellular growth and metastasis. Heparanase assays reported to-date are labor intensive, complex and/or expensive. A simpler assay is critically needed to understand the myriad roles of heparanase. We reasoned that fluorescent heparin could serve as an effective probe of heparanase levels. Following synthesis and screening, a heparin preparation labeled with DABCYL and EDANS was identified, which exhibited a characteristic increase in signal following cleavage by human heparanase. This work describes the synthesis of this heparin substrate, its kinetic and spectrofluorometric properties, optimization of the heparanase assay, use of the assay in inhibitor screening, and elucidation of the state of heparanase in different cell lines. Our FRET-based assay is much simpler and more robust than all assays reported in the literature as well as a commercially available kit.
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Affiliation(s)
- Jyothi C Sistla
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA; Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Shravan Morla
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA; Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Al-Humaidi B Alabbas
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA; Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Ravi C Kalathur
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Chetna Sharon
- Hunter Holmes McGuire VA Medical Center, Richmond, VA 23249, USA
| | - Bhaumik B Patel
- Hunter Holmes McGuire VA Medical Center, Richmond, VA 23249, USA; Division of Hematology, Oncology, and Palliative Care, Department of Internal Medicine and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Umesh R Desai
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA; Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA.
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45
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Sepuru KM, Nagarajan B, Desai UR, Rajarathnam K. Structural basis, stoichiometry, and thermodynamics of binding of the chemokines KC and MIP2 to the glycosaminoglycan heparin. J Biol Chem 2018; 293:17817-17828. [PMID: 30257866 DOI: 10.1074/jbc.ra118.004866] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 09/10/2018] [Indexed: 01/21/2023] Open
Abstract
Keratinocyte-derived chemokine (KC or mCXCL1) and macrophage inflammatory protein 2 (MIP2 or mCXCL2) play nonredundant roles in trafficking blood neutrophils to sites of infection and injury. The functional responses of KC and MIP2 are intimately coupled to their interactions with glycosaminoglycans (GAGs). GAG interactions orchestrate chemokine concentration gradients and modulate receptor activity, which together regulate neutrophil trafficking. Here, using NMR, molecular dynamics (MD) simulations, and isothermal titration calorimetry (ITC), we characterized the molecular basis of KC and MIP2 binding to the GAG heparin. Both chemokines reversibly exist as monomers and dimers, and the NMR analysis indicates that the dimer binds heparin with higher affinity. The ITC experiments indicate a stoichiometry of two GAGs per KC or MIP2 dimer and that the enthalpic and entropic contributions vary significantly between the two chemokine-heparin complexes. NMR-based structural models of heparin-KC and heparin-MIP2 complexes reveal that different combinations of residues from the N-loop, 40s turn, β3-strand, and C-terminal helix form a binding surface within a monomer and that both conserved residues and residues unique to a particular chemokine mediate the binding interactions. MD simulations indicate significant residue-specific differences in their contribution to binding and affinity for a given chemokine and between chemokines. On the basis of our observations that KC and MIP2 bind to GAG via distinct molecular interactions, we propose that the differences in these GAG interactions lead to differences in neutrophil recruitment and play nonoverlapping roles in resolution of inflammation.
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Affiliation(s)
- Krishna Mohan Sepuru
- From the Departments of Biochemistry and Molecular Biology; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555
| | - Balaji Nagarajan
- Department of Medicinal Chemistry and Institute for Structural Biology, and Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219
| | - Umesh R Desai
- Department of Medicinal Chemistry and Institute for Structural Biology, and Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219
| | - Krishna Rajarathnam
- From the Departments of Biochemistry and Molecular Biology; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555; Microbiology and Immunology.
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46
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Gangji RN, Sankaranarayanan NV, Elste J, Al-Horani RA, Afosah DK, Joshi R, Tiwari V, Desai UR. Inhibition of Herpes Simplex Virus-1 Entry into Human Cells by Nonsaccharide Glycosaminoglycan Mimetics. ACS Med Chem Lett 2018; 9:797-802. [PMID: 30128070 DOI: 10.1021/acsmedchemlett.7b00364] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Accepted: 07/16/2018] [Indexed: 01/29/2023] Open
Abstract
Although heparan sulfate (HS) has been implicated in facilitating entry of enveloped viruses including herpes simplex virus (HSV), small molecules that effectively compete with this abundant, cell surface macromolecule remain unknown. We reasoned that entry of HSV-1 involving its glycoprotein D (gD) binding to HS could be competitively targeted through small, synthetic, nonsaccharide glycosaminoglycan mimetics (NSGMs). Screening a library of NSGMs identified a small, distinct group that bound gD with affinities of 8-120 nM. Studies on HSV-1 entry into HeLa, HFF-1, and VK2/E6E7 cells identified inhibitors with potencies in the range of 0.4-1.0 μM. These synthetic NSGMs are likely to offer promising chemical biology probes and/or antiviral drug discovery opportunities.
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Affiliation(s)
- Rahaman Navaz Gangji
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
| | - Nehru Viji Sankaranarayanan
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - James Elste
- Department of Microbiology and Immunology, Chicago College of Osteopathic Medicine, Midwestern University, Downers Grove, Illinois 60515, United States
| | - Rami A. Al-Horani
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- College of Pharmacy, Xavier University of Louisiana, New Orleans, Louisiana 70125, United States
| | - Daniel K. Afosah
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Rachel Joshi
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Vaibhav Tiwari
- Department of Microbiology and Immunology, Chicago College of Osteopathic Medicine, Midwestern University, Downers Grove, Illinois 60515, United States
| | - Umesh R. Desai
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298, United States
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47
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Periasamy S, Lin CH, Nagarajan B, Sankaranarayanan NV, Desai UR, Liu MY. Mucoadhesive role of tamarind xyloglucan on inflammation attenuates ulcerative colitis. J Funct Foods 2018; 47:1-10. [PMID: 30555535 PMCID: PMC6289526 DOI: 10.1016/j.jff.2018.05.035] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Tamarind xyloglucan (TXG) is edible, bioavailable and mucoadhesive polysaccharide. The aim of this study was (i) to investigate molecular docking studies on the interaction of TXG to MUC1 and cytokine receptors and (ii) to assess the mucoadhesive role of TXG in UC. In vivo study: C57Bl6 mice were administered with DSS 3% (w/v) in drinking water; TXG 100 or 300 mg/kg/day was given orally for 7 days simultaneously. TXG consistently binds to MUC1 and cytokine receptors in molecular docking studies. TXG decreased the expression of MUC1 and MUC2. The mucoadhesive ability of TXG decreased IL-1β and IL-6 levels. Furthermore, TXG decreased the expression of TLR4, MyD88, I-κB and NF-κB thereby attenuating inflammation via TLR4/NF-κB signaling pathway. TXG mucoadhesion to MUC1 played a pivotal role in attenuating inflammation. To conclude, the mucoadhesive role of TXG is important in the attenuation of inflammation and healing of UC.
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Affiliation(s)
- Srinivasan Periasamy
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan 70428, Taiwan
| | - Chia-Hui Lin
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan 70428, Taiwan
| | - Balaji Nagarajan
- Institute for Structural Biology, Drug Discovery and Development and Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Nehru Viji Sankaranarayanan
- Institute for Structural Biology, Drug Discovery and Development and Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Umesh R. Desai
- Institute for Structural Biology, Drug Discovery and Development and Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Ming-Yie Liu
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan 70428, Taiwan
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48
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Tran DT, Zhang T, Stutsman R, Might M, Desai UR, Kuberan B. anexVis: visual analytics framework for analysis of RNA expression. Bioinformatics 2018; 34:2510-2512. [PMID: 29506198 DOI: 10.1093/bioinformatics/bty122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 02/28/2018] [Indexed: 01/22/2023] Open
Abstract
Summary Although RNA expression data are accumulating at a remarkable speed, gaining insights from them still requires laborious analyses, which hinder many biological and biomedical researchers. This report introduces a visual analytics framework that applies several well-known visualization techniques to leverage understanding of an RNA expression dataset. Our analyses on glycosaminoglycan-related genes have demonstrated the broad application of this tool, anexVis (analysis of RNA expression), to advance the understanding of tissue-specific glycosaminoglycan regulation and functions, and potentially other biological pathways. Availability and implementation The application is accessible at https://anexvis.chpc.utah.edu/, source codes deposited on GitHub. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Diem-Trang Tran
- Department of Medicinal Chemistry.,School of Computing, University of Utah, Salt Lake City, UT, USA
| | - Tian Zhang
- School of Computing, University of Utah, Salt Lake City, UT, USA
| | - Ryan Stutsman
- School of Computing, University of Utah, Salt Lake City, UT, USA
| | - Matthew Might
- Hugh Kaul Personalized Medicine Institute, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Umesh R Desai
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA, USA
| | - Balagurunathan Kuberan
- Department of Medicinal Chemistry.,Department of Biology, University of Utah, Salt Lake City, UT, USA
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49
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Boothello RS, Patel NJ, Damle PK, Sharon C, Chougoni KK, Desai UR, Grossman SR, Patel BB. Abstract 3460: p38-p14ARF-CtBP2 axis as a novel regulator of CSC phenotype and tumor cell dormancy. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-3460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Cancer cell dormancy and the cancer stem cell (CSC) phenotype are interlinked and play a crucial role in disease relapse. The pp38/pERK signaling ratio positively regulates cellular dormancy. We observed that heparin hexasaccharide (HS06) inhibited colon CSC self-renewal through isoform specific induction of pp38α/β, increasing the pp38/pERK ratio, and downregulation of C-terminal binding protein-2 (CtBP2) levels which is known to play a critical role in CSC growth. Hence, we hypothesized that HS06 inhibits CSCs self-renewal and prevents dormancy escape through regulation of CtBP2 in a manner dependent on p38 activation. Method: Spheroid culture of HT29 and HCT116 colon cancer cells was used for CSC self-renewal monitoring. Transient transfection with p38α, p14ARF, CtBP2 shRNA and/or expression vector with appropriate scrambled or vector controls was used to modulate cell signaling through this pathway. Standard western blotting, Q-PCR, flow cytometry, and immunoprecipitation were used to examine protein levels, their phosphorylation status and protein-protein interactions. Short term exposure of colon cancer cells (HT29) to chemotherapy (5-Fluorouracil (125μM) and oxaliplatin (5μM) (5-FUOX)) was used to study a transient dormancy-like state followed by growth escape. HT29 CSC (1x105 CD133+/CXCR4+ cells) induced xenografts were established s.c. in NCr nude mice were treated with HS06 (150mg/kg 3xwk., 3 weeks) and monitored for tumor growth, and xenografts were analyzed for CSC makers and p38-p14ARF-CtBP2 axis status. Results: HS06 inhibited CtBP2 levels but increased the expression of its negative regulator p14 ARF in vitro and in vivo in a manner dependent on p38 activation, as SB203580, a selective p38α/β inhibitor, as well as p38α shRNA, both near-completely reversed the effects of HS06 on p14ARF, CtBP2, and CSC self-renewal. This regulation of p14ARF and CtBP2 was post-transcriptional in nature. Moreover, reciprocal coimmunoprecipitation studies revealed a novel physical interaction between endogenous pp38 and p14ARF, which resulted in serine phosphorylation of p14ARF in a p38 activation-dependent manner that was critical for regulation of CtBP2 levels and CSC self-renewal. Using a chemotherapy induced cellular dormancy model, we observed that activation/upregulation of p38 and p14ARF prevented escape from dormancy in vitro, whereas increased CtBP2 had the opposite effect. Conclusion: We have discovered a novel p38-p14ARF-CtBP2 axis that plays a dual role in colon cancer CSC self-renewal and cellular dormancy. Agents targeting this pathway e.g., HS06 and CtBP2 inhibitors, represent novel therapeutic strategies to inhibit CSCs and prevent dormancy escape leading to reduced tumor relapse and/or cure.
Citation Format: Rio S. Boothello, Nirmita J. Patel, Priyadarshan K. Damle, Chetna Sharon, Kranthi Kumar Chougoni, Umesh R. Desai, Steven R. Grossman, Bhaumik B. Patel. p38-p14ARF-CtBP2 axis as a novel regulator of CSC phenotype and tumor cell dormancy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3460.
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Kummarapurugu AB, Afosah DK, Sankaranarayanan NV, Navaz Gangji R, Zheng S, Kennedy T, Rubin BK, Voynow JA, Desai UR. Molecular principles for heparin oligosaccharide-based inhibition of neutrophil elastase in cystic fibrosis. J Biol Chem 2018; 293:12480-12490. [PMID: 29903912 DOI: 10.1074/jbc.ra118.002644] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 06/12/2018] [Indexed: 11/06/2022] Open
Abstract
Cystic fibrosis (CF) is a multifactorial disease in which dysfunction of protease-antiprotease balance plays a key role. The current CF therapy relies on dornase α, hypertonic saline, and antibiotics and does not address the high neutrophil elastase (NE) activity observed in the lung and sputum of CF patients. Our hypothesis is that variants of heparin, which potently inhibit NE but are not anticoagulant, would help restore the protease-antiprotease balance in CF. To realize this concept, we studied molecular principles governing the effectiveness of different heparins, especially 2-O,3-O-desulfated heparin (ODSH), in the presence of sputum components and therapeutic agents. Using sputa from CF patients and an NE activity assay, we found that heparins are ineffective if used in the absence of dornase. This is true even when mucolytics, such as DTT or N-acetylcysteine, were used. Computational modeling suggested that ODSH and DNA compete for binding to an overlapping allosteric site on NE, which reduces the anti-NE potential of ODSH. NE inhibition of both DNA and ODSH is chain length-dependent, but ODSH chains exhibit higher potency per unit residue length. Likewise, ODSH chains exhibit higher NE inhibition potential compared with DNA chains in the presence of saline. These studies suggest fundamental differences in DNA and ODSH recognition and inhibition of NE despite engaging overlapping sites and offer unique insights into molecular principles that could be used in developing antiprotease agents in the presence of current treatments, such as dornase and hypertonic saline.
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Affiliation(s)
- Apparao B Kummarapurugu
- From the Children's Hospital of Richmond at Virginia Commonwealth University, Richmond, Virginia 23298
| | - Daniel K Afosah
- the Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298.,the Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23298, and
| | - Nehru Viji Sankaranarayanan
- the Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298.,the Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23298, and
| | - Rahaman Navaz Gangji
- the Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23298, and
| | - Shuo Zheng
- From the Children's Hospital of Richmond at Virginia Commonwealth University, Richmond, Virginia 23298
| | - Thomas Kennedy
- the Tulane University Medical Center, New Orleans, Louisiana 70112
| | - Bruce K Rubin
- From the Children's Hospital of Richmond at Virginia Commonwealth University, Richmond, Virginia 23298
| | - Judith A Voynow
- From the Children's Hospital of Richmond at Virginia Commonwealth University, Richmond, Virginia 23298,
| | - Umesh R Desai
- the Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298, .,the Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23298, and
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