scholarly journals Structural Basis of Antibody Conformation and Stability Modulation by Framework Somatic Hypermutation

2022 ◽  
Vol 12 ◽  
Author(s):  
Zizhang Sheng ◽  
Jude S. Bimela ◽  
Phinikoula S. Katsamba ◽  
Saurabh D. Patel ◽  
Yicheng Guo ◽  
...  

Accumulation of somatic hypermutation (SHM) is the primary mechanism to enhance the binding affinity of antibodies to antigens in vivo. However, the structural basis of the effects of many SHMs remains elusive. Here, we integrated atomistic molecular dynamics (MD) simulation and data mining to build a high-throughput structural bioinformatics pipeline to study the effects of individual and combination SHMs on antibody conformation, flexibility, stability, and affinity. By applying this pipeline, we characterized a common mechanism of modulation of heavy-light pairing orientation by frequent SHMs at framework positions 39H, 91H, 38L, and 87L through disruption of a conserved hydrogen-bond network. Q39LH alone and in combination with light chain framework 4 (FWR4L) insertions further modulated the elbow angle between variable and constant domains of many antibodies, resulting in improved binding affinity for a subset of anti-HIV-1 antibodies. Q39LH also alleviated aggregation induced by FWR4L insertion, suggesting remote epistasis between these SHMs. Altogether, this study provides tools and insights for understanding antibody affinity maturation and for engineering functionally improved antibodies.

2018 ◽  
Vol 92 (18) ◽  
Author(s):  
Kun-Wei Chan ◽  
Ruimin Pan ◽  
Matthew Costa ◽  
Miroslaw K. Gorny ◽  
Shixia Wang ◽  
...  

ABSTRACTElucidating the structural basis of antibody (Ab) gene usage and affinity maturation of vaccine-induced Abs can inform the design of immunogens for inducing desired Ab responses in HIV vaccine development. Analyses of monoclonal Abs (MAbs) encoded by the same immunoglobulin genes at different stages of maturation can help to elucidate the maturation process. We have analyzed four human anti-V3 MAbs with the same VH1-3*01 and VL3-10*01 gene usage. Two MAbs, TA6 and TA7, were developed from a vaccinee in the HIV vaccine phase I trial DP6-001 with a polyvalent DNA prime/protein boost regimen, and two others, 311-11D and 1334, were developed from HIV-infected patients. The somatic hypermutation (SHM) rates in VH of vaccine-induced MAbs are lower than in chronic HIV infection-induced MAbs, while those in VL are comparable. Crystal structures of the antigen-binding fragments (Fabs) in complex with V3 peptides show that these MAbs bind the V3 epitope with a new cradle-binding mode and that the V3 β-hairpin lies along the antigen-binding groove, which consists of residues from both heavy and light chains. Residues conserved from the germ line sequences form specific binding pockets accommodating conserved structural elements of the V3 crown hairpin, predetermining the Ab gene selection, while somatically mutated residues create additional hydrogen bonds, electrostatic interactions, and van der Waals contacts, correlating with an increased binding affinity. Our data provide a unique example of germ line sequences determining the primordial antigen-binding sites and SHMs correlating with affinity maturation of Abs induced by vaccine and natural HIV infection.IMPORTANCEUnderstanding the structural basis of gene usage and affinity maturation for anti-HIV-1 antibodies may help vaccine design and development. Antibodies targeting the highly immunogenic third variable loop (V3) of HIV-1 gp120 provide a unique opportunity for detailed structural investigations. By comparing the sequences and structures of four anti-V3 MAbs at different stages of affinity maturation but of the same V gene usage, two induced by vaccination and another two by chronic infection, we provide a fine example of how germ line sequence determines the essential elements for epitope recognition and how affinity maturation improves the antibody's recognition of its epitope.


2009 ◽  
Vol 206 (13) ◽  
pp. 2907-2914 ◽  
Author(s):  
Tanja A. Schwickert ◽  
Boris Alabyev ◽  
Tim Manser ◽  
Michel C. Nussenzweig

Germinal centers (GCs) are specialized structures in which B lymphocytes undergo clonal expansion, class switch recombination, somatic hypermutation, and affinity maturation. Although these structures were previously thought to contain a limited number of isolated B cell clones, recent in vivo imaging studies revealed that they are in fact dynamic and appear to be open to their environment. We demonstrate that B cells can colonize heterologous GCs. Invasion of primary GCs after subsequent immunization is most efficient when T cell help is shared by the two immune responses; however, it also occurs when the immune responses are entirely unrelated. We conclude that GCs are dynamic anatomical structures that can be reutilized by newly activated B cells during immune responses.


Author(s):  
Melappa Govindappa ◽  
V. Thanuja ◽  
S. Tejashree ◽  
C.A. Soukhya ◽  
Suresh Barge ◽  
...  

The present work was aimed to identify phytochemicals in C. uredinicola methanol extract from qualitative, TLC and GC-MS method and evaluated for antioxidant, anti-HIV, anti-diabetes, anti-cholinesterase activity in vitro and in silico. The C. uredinicola extract showed flavonoids, tannins, alkaloids, glycosides, phenols, terpenoids, and coumarins presence in qualitative method. From GC-MS analysis, identified seven different phytochemicals and out of seven, four (coumarin, coumarilic acid, hymecromone, alloisoimperatorin) are coumarins. The C. uredinicola extract have shown significant antioxidant activity in DPPH (73) and FRAP (1359) method. The HIV-1 RT (83.81+2.14), gp 120 (80.24+2.31), integrase (79.43+3.14) and protease (77.63+2.14), DPPIV, β-glucosidase and acetyl cholinesterase activity was significantly reduced by the extract. The 2-diphenylmethyleneamino methyl ester had shown significant interaction with oxidant and HIV-1 proteins whereas alloisoimperatorin have interacted with diabetes and cholinesterase proteins followed by hymecromone with high binding energy. These three phytochemicals are non-carcinogens, non-toxic, readily degradable and have drug likeliness properties. The C. uredinicola phytochemicals are responsible for management of diabetes, HIV-1 and Alzheimer. Further in vivo work is needed to justify our research.


Nanomedicine ◽  
2021 ◽  
Author(s):  
Samrajya Lakshmi Yeruva ◽  
Prashant Kumar ◽  
Seetharam Deepa ◽  
Anand K Kondapi

Aim: We report here the development of tenofovir- and curcumin-loaded lactoferrin nanoparticles (TCNPs) as an HIV-microbicide. Materials & methods: TCNPs were subjected to various physicochemical characterization experiments, followed by in vitro and in vivo experiments to assess their efficacy. Results: TCNPs had a diameter of 74.31 ± 2.56 nm with a gross encapsulation of more than 61% for each drug. Nanoparticles were effective against HIV-1 replication, with an IC50 of 1.75 μM for curcumin and 2.8 μM for tenofovir. TCNPs provided drug release at the application site for up to 8–12 h, with minimal leakage into the systemic circulation. TCNPs showed spermicidal activity at ≥200 μM and induced minimal cytotoxicity and inflammation in the vaginal epithelium as revealed by histopathological and ELISA studies. Conclusion: We demonstrated that TCNPs could serve as a novel anti-HIV microbicidal agent in rats. [Formula: see text]


2003 ◽  
Vol 77 (22) ◽  
pp. 12057-12066 ◽  
Author(s):  
Yanjie Yi ◽  
Anjali Singh ◽  
Farida Shaheen ◽  
Andrew Louden ◽  
ChuHee Lee ◽  
...  

ABSTRACT Macrophagetropic R5 human immunodeficiency virus type 1 (HIV-1) isolates often evolve into dualtropic R5X4 variants during disease progression. The structural basis for CCR5 coreceptor function has been studied in a limited number of prototype strains and suggests that R5 and R5X4 Envs interact differently with CCR5. However, differences between unrelated viruses may reflect strain-specific factors and do not necessarily represent changes resulting from R5 to R5X4 evolution of a virus in vivo. Here we addressed CCR5 domains involved in fusion for a large set of closely related yet functionally distinct variants within a primary isolate swarm, employing R5 and R5X4 Envs derived from the HIV-1 89.6PI quasispecies. R5 variants of 89.6PI could fuse using either N-terminal or extracellular loop CCR5 sequences in the context of CCR5/CXCR2 chimeras, similar to the unrelated R5 strain JRFL, but R5X4 variants of 89.6PI were highly dependent on the CCR5 N terminus. Similarly, R5 89.6PI variants and isolate JRFL tolerated N-terminal CCR5 deletions, but fusion by most R5X4 variants was markedly impaired. R5 89.6PI Envs also tolerated multiple extracellular domain substitutions, while R5X4 variants did not. In contrast to CCR5 use, fusion by R5X4 variants of 89.6PI was largely independent of the CXCR4 N-terminal region. Thus, R5 and R5X4 species from a single swarm differ in how they interact with CCR5. These results suggest that R5 Envs possess a highly plastic capacity to interact with multiple CCR5 regions and support the concept that viral evolution in vivo results from the emergence of R5X4 variants with the capacity to use the CXCR4 extracellular loops but demonstrate less-flexible interactions with CCR5 that are strongly dependent on the N-terminal region.


Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 4823-4823
Author(s):  
Nowah K. A. Afangbedji ◽  
Namita Kumari ◽  
Dymtro Kowalskyy ◽  
Sergei Nekhai

Abstract Background Iron chelators are used in the treatment of iron overload related diseases and are currently receiving a major attention as potential antitumor drugs. In recent studies, the antitumor activity of thiosemicarbazones-class of iron chelator, including Di-2-pyridilketone-4,4- dimethyl-3-thiosemicarbazone (Dp44mT) has been investigated in over 20 phase I and II clinical trials [1, 2,3]. Iron chelators were also considered as anti-HIV-1 agents. However, the main obstacle to using iron chelators in vivois the deleterious side effect of methemoglobinemia induced by some iron chelators that are able to scavenge electrons from the heme-bound iron in hemoglobin. In our previous studies, we developed novel phenyl-1-pyridin-2yl-ethanone (PPY)-based iron chelators that we showed to increase IKBα expression, modulate CDK2 and CDK9 activities and inhibit HIV-1 [4]. Objective Our objective was to test the effect of PPYeT iron chelator for methemoglobin induction. The methemoglobin induction effect was compared with several additional iron chelators including Di-2-pyridylketone-4,4-dimethyl-3-thiosemicarbazone (Dp44mT) and PPY analogues. Methods Fluorometric analysis was carried out in promonocytic THP-1 cells to evaluate the ability of our novel PPYeT iron chelator to reduce labile iron pool (LIP). The effect of PPYet on LIP was compared to the effect to SIH. Subsequently, spectrophotometric analysis was used to measure and quantify the production of methemoglobin in human red blood cells lysates and in isolated intact human red blood cells treated with PPYeT and various other iron chelators including DP44mT and DP4mT. Results PPYeT significantly reduced LIP in THP-1 cells overloaded with iron comparing to the cells treated with SIH. In RBC lysates and in intact RBC, PPYeT treatment showed notably lesser production of methemoglobin in comparison to DP44mT and DP4mT chelators. In RBC lysates, PPYeT produced about four-fold less methemoglobin than Dp44mT and ten-fold less than Dp4mT. Conclusion The novel compound, PPYeT, shows a remarkably low ability to catalyze the formation of methemoglobin in human RBC lysates and also in intact RBCs as compared to Dp44mT. These findings indicate that PPYeT may be useful for future in vivo studies as it produces less methemoglobinemia. Further studies will evaluate the effect PPYeT as anti-cancer or anti HIV-1 inhibitor in vivo. Acknowledgments This work was supported by NIH Research Grants 1P50HL118006, 1R01HL125005, and 5G12MD007597. The content is solely the responsibility of the authors and does not necessarily represent the official view of NHLBI, NIMHD or NIH. References 1. Richardson, D. R.; Sharpe, P. C.; Lovejoy, D. B.; Senaratne, D.; Kalinowski, D. S.; Islam, M.; Bernhardt, P. V. Dipyridyl Thiosemicarbazone Chelators with Potent and Selective Antitumor Activity Form Iron Complexes with Redox Activity. Journal of Medicinal Chemistry. 2006, 49, 6510−6521 2-Yuan, J.; Lovejoy, D. B.; Richardson, D. R. Novel Di-2-pyridylDerived Iron Chelators with Marked and Selective Antitumor Activity: In Vitro and in Vivo Assessment. Blood2004, 104, 1450−1458. 3-Whitnall, M.; Howard, J.; Ponka, P.; Richardson, D. R. A Class of Iron Chelators with a Wide Spectrum of Potent Antitumor Activity that Overcomes Resistance to Chemotherapeutics. Proceedings of National Academy of Science. U. S. A.2006, 103, 14901−14906. 4. Kumari N, Iordanskiy S, Kovalskyy D, Breuer D, Niu X, Lin X, Xu M, Gavrilenko K, Kashanchi F, Dhawan S et al: Phenyl-1-Pyridin-2yl-ethanone-based iron chelators increase IkappaB-alpha expression, modulate CDK2 and CDK9 activities, and inhibit HIV-1 transcription. Antimicrob Agents Chemother 2014, 58(11):6558-6571. Disclosures No relevant conflicts of interest to declare.


2011 ◽  
Vol 22 (2) ◽  
pp. 57-65 ◽  
Author(s):  
Yohei Isono ◽  
Norikazu Sakakibara ◽  
Paula Ordonez ◽  
Takayuki Hamasaki ◽  
Masanori Baba ◽  
...  

Background: Nine novel uracil analogues were synthesized and evaluated as inhibitors of HIV-1. Methods: Key structural modifications included replacement of the 6-chloro group of 1-benzyl-6-chloro-3-(3,5-dimethylbenzyl)uracil by other functional groups or N1-alkylation of 3-(3,5-dimethylbenzyl)-5-fluorouracil. Results: These compounds showed only micromolar potency against HIV-1 in MT-4, though two of them; 6-azido-1-benzyl-3-(3,5-dimethylbenzyl) uracil and 6-amino-1-benzyl-3-(3,5-dimethylbenzyl) uracil were highly potent (half maximal effective concentration =0.067 and 0.069 μM) and selective (selectivity index =685 and 661), respectively. Structure–activity relationships among the newly synthesized uracil analogues suggest the importance of the H-bond formed between 6-amino group of 6-amino-1-benzyl-3-(3,5-dimethylbenzyl) uracil and amide group of HIV-1 reverse transcriptase. Conclusions: We discovered two 6-substituted 1-benzyl-3-(3,5-dimethylbenzyl) uracils, (6-azido-1-benzyl-3-(3,5-dimethylbenzyl) uracil and 6-amino-1-benzyl-3-(3,5-dimethylbenzyl) uracil) as novel anti-HIV agents. These compounds should be further pursued for their toxicity and pharmacokinetics in vivo as well as antiviral activity against non-nucleoside reverse transcriptase inhibitor-resistant strains.


2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Kaifan Dai ◽  
Salar N Khan ◽  
Yimeng Wang ◽  
Linling He ◽  
Javier Guenaga ◽  
...  
Keyword(s):  

Author(s):  
Brigette Tippin ◽  
Myron F. Goodman

The mechanism of somatic hypermutation of the immunoglobulin genes remains a mystery after nearly 30 years of intensive research in the field. While many clues to the process have been discovered in terms of the genetic elements required in the immunoglobulin genes, the key enzymatic players that mediate the introduction of mutations into the variable region are unknown. The recent wave of newly discovered eukaryotic DNA polymerases have given a fresh supply of potential candidates and a renewed vigour in the search for the elusive mutator factor governing affinity maturation. In this paper, we discuss the relevant genetic and biochemical evidence known to date regarding both somatic hypermutation and the new DNA polymerases and address how the two fields can be brought together to identify the strongest candidates for further study. In particular we discuss evidence for the in vitro biochemical misincorporation properties of human Rad30B/Pol ι and how it compares to the in vivo somatic hypermutation spectra.


2013 ◽  
Vol 9 (10) ◽  
pp. 2253-2262 ◽  
Author(s):  
Kar Muthumani ◽  
Seleeke Flingai ◽  
Megan Wise ◽  
Colleen Tingey ◽  
Kenneth E Ugen ◽  
...  

Sign in / Sign up

Export Citation Format

Share Document