27. Vishwambhar Bhandare, Bajarang Vasant Kumbhar and Ambarish Kunwar, Differential binding affinity of tau repeat region R2 with neuronal specific β-tubulin isotypes, Scientific Reports, Accepted (2019)
Tau is a microtubule-associated protein whose C-terminal domain consisting of four repeat regions R1, R2, R3 and R4 binds to microtubules to stabilize them. In several neurodegenerative diseases, tau detaches from microtubules to form insoluble aggregates leading to tauopathy. Tubulin isotypes show tissue specific expression as their relative proportion varies significantly in different type of cells. It is also known that tau binds differently to different cell lines and can either promote or demote microtubule polymerization. However, the relative binding affinity of tau to the different β-tubulin isotypes present in different cell lines is completely unknown. Therefore, we studied relative binding affinity of Tau repeat region R2 to neuronal specific tubulin isotypes βI, βIIb, and βIII using molecular modelling approach and found that the order of binding energy of tau with tubulin is βIII > βIIb > βI. Our strategy can be potentially adapted to understand differential binding affinity of tau towards beta tubulin isotypes present in other cell lines.
26. Carlos M. Guardia, Raffaella De Pace, Aritra Sen, Amra Saric, Michal Jarnik, David A. Kolin, Ambarish Kunwar, Juan S. Bonifacino, Reversible association with motor proteins (RAMP): A streptavidin-based method to manipulate organelle positioning, PLoS Biology 17(5): e3000279 (2019)
A new method, named reversible association with motor proteins (RAMP) has been developed and characterized for manipulation of organelle positioning within the cytoplasm. RAMP consists of coexpressing in cultured cells (i) an organellar protein fused to the streptavidin-binding peptide (SBP) and (ii) motor, neck, and coiled-coil domains from a plus-end–directed or minus-end–directed kinesin fused to streptavidin. The SBP–streptavidin interaction drives accumulation of organelles at the plus or minus end of microtubules, respectively. Importantly, competition of the streptavidin–SBP interaction by the addition of biotin to the culture medium rapidly dissociates the motor construct from the organelle, allowing restoration of normal patterns of organelle transport and distribution. A distinctive feature of this method is that organelles initially accumulate at either end of the microtubule network in the initial state and are subsequently released from this accumulation, allowing analyses of the movement of a synchronized population of organelles by endogenous motors.
25. Bajarang Vasant Kumbhar, Vishwambhar Bhandare, Dulal Panda and Ambarish Kunwar, Delineating the Interaction of Combretastatin A-4 with αβ tubulin Isotypes present in Drug Resistant Human Lung Carcinoma using a Molecular Modeling Approach, Journal of Biomolecular Structure and Dynamics, DOI: 10.1080/07391102.2019.1577174 (2019)
Tubulin isotypes are known to regulate microtubule dynamic instability and contribute to the development of drug resistance in certain types of cancers. Combretastatin-A4 (CA-4) has apotent anti-mitotic, vascular disrupting and anti-angiogenic activity. It binds at the interface of αβ tubulin heterodimers and inhibits microtubules assembly. Interestingly, the CA-4 resistant human lung carcinoma shows alteration of βI and βIII isotype levels, a higher expression of βI tubulin isotype and a decreased expression of βIII tubulin isotypes has been reported in drug resistant cell lines. However, the origin of CA-4 resistance in lung carcinoma is not well understood. Our results suggest that drug resistance is induced in human lung carcinoma cells by altering the expression of β-tubulin isotypes namely βI and βIII which show lowest binding affinities. Our present study can help in designing potential CA-4 analogs against drug-resistant cancer cells showing altered expression of tubulin isotypes.
24. Bajarang Vasant Kumbhar, Dulal Panda and Ambarish Kunwar, Interaction of microtubule depolymerizing agent indanocine with different human αβ tubulin isotypes, PLoS ONE 13(3): e0194934 (2018)
2015 Journal Impact Factor = 3.057
Tubulin isotypes are known to regulate the stability and dynamics of microtubules, and are also involved in the development of resistance against microtubule-targeted cancer drugs. Indanocine, a potent microtubule depolymerizing agent, is highly active against multidrug-resistant (MDR) cancer cells without affecting normal cells. It is known to disrupt microtubule dynamics in cells and induce apoptotic cell death. Indanocine is reported to bind to tubulin at the colchicine site i.e. at the interface of αβ tubulin heterodimer. However, it’s precise binding mode, involved molecular interactions and the binding affinities with different αβ-tubulin isotypes present in MDR cells are not well understood. Here, the binding affinities of human αβ-tubulin isotypes with indanocine were examined, employing the molecular modeling approach i.e. docking, molecular dynamics simulation and binding energy calculations. Our study provides a significant understanding of involved molecular interactions of indanocine with tubulin isotypes, which may help to design potent indanocine analogues for specific tubulin isotypes in MDR cells in future.
23. Anjneya Takshak, Tanushree Roy, Parag Tandaiya and Ambarish Kunwar, Effect of Fuel Concentration and Force on Collective Transport by a Team of Dynein Motors, Protein Science, Vol. 26, 186–197 (2017)
2015 Journal Impact Factor = 3.039
Motor proteins are essential components of intracellular transport inside eukaryotic cells. These protein molecules use chemical energy obtained from hydrolysis of ATP to produce mechanical forces required for transporting cargos inside cells, from one location to another, in a directed manner. Of these motors, cytoplasmic dynein is structurally more complex than other motor proteins involved in intracellular transport, as it shows force and fuel (ATP) concentration dependent step-size. Cytoplasmic dynein motors are known to work in a team during cargo transport and force generation. Here, we use a complete Monte-Carlo model of single dynein constrained by in-vitro experiments, which includes the effect of both force and ATP on stepping as well as detachment of motors under force. We then use our complete Monte-Carlo model of single dynein motor to understand collective cargo transport by a team of dynein motors, such as dependence of cargo travel distance and velocity on applied force and fuel concentration.
22. Anjneya Takshak, Nirvantosh Mishra, Aditi S Kulkarni, Ambarish Kunwar, Effect of Fuel Concentration on Cargo Transport by a Team of Kinesin Motors, Physica A, Vol. 467, 395–406 (2017)
2015 Journal Impact Factor = 1.785
Eukaryotic cells employ specialized proteins called molecular motors for transporting organelles and vesicles from one location to another in a regulated and directed manner. These molecular motors often work collectively in a team while transporting cargos. Molecular motors use cytoplasmic ATP as fuel, which is hydrolyzed to generate mechanical force. While the effect of ATP concentration on cargo transport by single Kinesin motor function is well understood, it is still unexplored, both theoretically and experimentally, how ATP concentration would affect cargo transport by a team of Kinesin motors. For instance, how does fuel concentration affect the travel distances and travel velocities of cargo? How cooperativity of Kinesin motors engaged on a cargo is affected by ATP concentration? To answer these questions, here we develop mechano-chemical models of cargo transport by a team of Kinesin motors. Our new results can be potentially useful in controlling artificial nano-molecular shuttles precisely for targeted delivery in various nano-technological applications.
21. Rajan Kumar Pandey, Bajrang Vashant Kumbhar, Shyam Sundar, Ambarish Kunwar and Vijay Kumar Prajapati, Structure based virtual screening, molecular docking, ADMET and molecular simulations to develop benzoxaborole analogues as potential inhibitor against Leishmania donovani trypanothione reductase, Journal of Receptors and Signal Transduction, Vol. 37, 60-70 (2017)
2015 Journal Impact Factor = 1.782
Visceral leishmaniasis (VL) is the most fatal form of leishmaniasis and it affects 70 countries worldwide. Increasing drug resistant for antileishmanial drugs such as miltefosine, sodium stibogluconate and pentamidine has been reported in the VL endemic region. To control the VL infection in the affected countries, it is necessary to develop new antileishmanial compounds with high efficacy and negligible toxicity. Computer aided programs such as binding free energy estimation; ADMET prediction and molecular dynamics simulation can be used to investigate novel antileishmanial molecules in shorter duration. In this study, we performed virtual screening of 1,160 benzoxaborole analogues along with reference inhibitors against trypanothione reductase of Leishmania parasite to develop anti-leishmanial lead molecule. The presented drug discovery based on computational study confirm that BOB27 can be used as a potential drug candidate and warrants further experimental investigation to fight against VL in endemic areas.
20. Rajan Kumar Pandey, Bajarang Vasant Kumbhar, Shubham Srivastava, Ruchi Malik, Shyam Sundar, Ambarish Kunwar and Vijay Kumar Prajapati, Febrifugine analogues as Leishmaniadonovani trypanothione reductase inhibitors: binding energy analysis assisted by molecular docking, ADMET and molecular dynamics simulation, Journal of Biomolecular Structure and Dynamics, Vol. 35, 141-158 (2017)
2015 Journal Impact Factor = 2.300
Visceral leishmaniasis (VL) affects people from 70 countries worldwide, mostly from Indian, African and south American continent. The increasing resistance to antimonial, miltefosine and frequent toxicity of amphotericin B drives an urgent need to develop an antileishmanial drug with excellent efficacy and safety profile. In this study we used molecular docking, ADMET and molecular dynamics simulation to confirm that that 6-chloro-3-[3-(3-hydroxy-2-piperidyl)-2-oxo-propyl]-7-(4-pyridyl) quinazolin-4-one can be potential drug candidate to fight against Leishmaniadonovani parasites.
19. Weili Hong, Anjneya Takshak, Olaolu Osunbayo, Ambarish Kunwar and Michael Vershinin, The Effect of Temperature on Microtubule-Based Transport by Cytoplasmic Dynein and Kinesin-1 Motors, Biophysical Journal, Vol. 111, 1287 (2016)
2015 Journal Impact Factor = 3.632
Cytoplasmic dynein and kinesin are both microtubule-based molecular motors but are structurally and evolutionarily unrelated. Under standard conditions, both move with comparable unloaded velocities toward either the microtubule minus (dynein) or plus (most kinesins) end. This similarity is important because it is often implicitly incorporated into models that examine the balance of cargo fluxes in cells and into models of the bidirectional motility of individual cargos. We examined whether this similarity is a robust feature, and specifically whether it persists across the biologically relevant temperature range. The velocity of mammalian cytoplasmic dynein, but not of mammalian kinesin-1, exhibited a break from simple Arrhenius behavior below 15°C—just above the restrictive temperature of mammalian fast axonal transport. In contrast, the velocity of yeast cytoplasmic dynein showed a break from Arrhenius behavior at a lower temperature (∼8°C). Our studies implicate cytoplasmic dynein as a more thermally tunable motor and therefore a potential thermal regulator of microtubule-based transport. Our theoretical analysis further suggests that motor velocity changes can lead to qualitative changes in individual cargo motion and hence net intracellular cargo fluxes.
18. Bajarang Vasant Kumbhar, Anubhaw Borogaon, Dulal Panda and Ambarish Kunwar, Exploring the Origin of Differential Binding Affinities of Human Tubulin Isotypes αβII, αβIII and αβIV for DAMA-colchicine using Homology Modelling, Molecular Docking and Molecular Dynamics Simulation, PLoS ONE 11(5): e0156048 (2016)
2015 Journal Impact Factor = 3.057
Tubulin isotypes are found to play an important role in regulating microtubule dynamics. The isotype composition is also thought to contribute in the development of drug resistance as tubulin isotypes show differential binding affinities for various anti-cancer agents. Tubulin isotypes αβII, αβIII and αβIV show differential binding affinity for colchicine. However, the origin of differential binding affinity is not well understood at the molecular level. In this paper, we investigate the origin of differential binding affinity of a colchicine analogue N-deacetyl-N-(2-mercaptoacetyl)-colchicine (DAMA-colchicine) for human αβII, αβIII and αβIV isotypes, employing sequence analysis, homology modeling, molecular docking, molecular dynamics simulation and MM-GBSA binding free energy calculations. Our computational approaches provide an insight into the effect of residue variations on differential binding of αβII, αβIII and αβIV tubulin isotypes with DAMA-colchicine and may help to design new analogues with higher binding affinities for tubulin isotypes.
17. Hanumant Pratap Singh, Anjneya Takshak, Utkarsh Mall and Ambarish Kunwar, Sliding of Microtubules by A Team of Dynein motors: Understanding the Effect of Spatial Distribution of Motor Tails and Mutual Exclusion of Motor Heads on Microtubules, International Journal of Modern Physics C, Vol. 27, 1650137 (2016)
2015 Journal Impact Factor = 1.195
Cytoplasmic dynein motors often work collectively as a team to drive important processes such as axonal growth, proplatelet formation and mitosis, as forces generated by single motors are insufficient. A large team of dynein motors is used to slide cytoskeletal microtubules with respect to one another during the process of proplatelet formation and axonal growth. Here we use a computational stochastic model where we model each dynein motor explicitly. In our model, we use both random as well as uniform distribution of dynein motors on cargo microtubule, as well as mutual exclusion of motors on microtubule tracks. We find that sliding velocities are least affected by the distribution of motor tails on microtubules, whereas they are greatly affected by mutual exclusion of motor heads on microtubule tracks. We also find that sliding velocity depends on the length of cargo microtubule if mutual exclusion among motor heads is considered.
16. Anjneya Takshak and Ambarish Kunwar, Importance of anisotropy in detachment rates for force production and cargo transport by a team of motor proteins, Protein Science, Vol. 25, 1075 (2016)
2015 Journal Impact Factor = 3.039
Many cellular processes are driven by collective forces generated by a team consisting of multiple molecular motor proteins. One aspect that has received less attention is the detachment rate of molecular motors under mechanical force/load. While detachment rate of kinesin motors measured under backward force increases rapidly for forces beyond stall-force; this scenario is just reversed for non-yeast dynein motors where detachment rate from microtubule decreases, exhibiting a catch-bond type behavior. It has been shown recently that yeast dynein responds anisotropically to applied load i.e. detachment rates are different under forward and backward pulling. Here, we use computational modeling to show that these anisotropic detachment rates might help yeast dynein motors to improve their collective force generation in the absence of catch-bond behavior. We further show that the travel distance of cargos would be longer if detachment rates are anisotropic. Our results suggest that anisotropic detachment rates could be an alternative strategy for motors to improve the transport properties and force production by the team.
15. Aijaz Rashid , Annapurna Kuppa , Ambarish Kunwar and Dulal Panda, Thalidomide (5HPP-33) suppresses microtubule dynamics and depolymerizes microtubule network by binding at vinblastine binding site on tubulin, Biochemistry, Vol. 54, 2149 (2015)
2015 Journal Impact Factor = 2.876
Thalidomides were initially thought to be broad range drugs specially to cure insomnia and to relieve morning sickness in pregnant women. However, its use was discontinued because of a major drawback of causing teratogenicity. In this study, we found that a thalidomide derivative, (5-hydroxy-2-(2,6-diisopropylphenyl)-1H-isoindole-1,3-dione) (5HPP-33) inhibited the proliferation of MCF-7. 5HPP-33 depolymerized microtubules and inhibited the reassembly of cold-depolymerized microtubules in MCF-7 cells. Molecular docking analysis suggested that 5HPP-33 shares its binding site on tubulin with vinblastine. The results provide a significant insight into the anti-mitotic mechanism of action of 5HPP-33 and also suggest a possible mechanism for the teratogenicity of thalidomides.
14. Roop Mallik, Arpan Kumar Rai, Pradeep Barak, Ashim Rai and Ambarish Kunwar, Teamwork in Microtubule Motors, Trends in Cell Biology,Vol. 23, 575 (2013)
2015 Journal Impact Factor = 11.532
Collective forces generated by a team consisting of multiple motor proteins drive diverse cellular processes. Here we review how the biophysical properties of single motors, and differences therein, may translate into collective motor function during organelle transport and perhaps in other processes outside transport.
15. Jubina Balan Venghateri, Tilak Kumar Gupta, Paul J Verma, Ambarish Kunwar and Dulal Panda, Ansamitocin P3 depolymerizes microtubules and induces apoptosis by binding to tubulin at the vinblastine site, PLoS ONE 8(10): e75182. doi:10.1371/journal.pone.0075182 (2013)
2012 Journal Impact Factor = 3.057
In this paper, we have elucidated the mechanism of action of ansamitocin P3, a structural analogue of maytansine for its anticancer activity. Ansamitocin P3 potently inhibited the proliferation of MCF-7, HeLa, EMT-6/AR1 and MDA-MB-231 cells in culture. Ansamitocin P3 strongly depolymerized both interphase and mitotic microtubules and perturbed chromosome segregation at its proliferation inhibitory concentration range. Treatment of ansamitocin P3 activated spindle checkpoint surveillance proteins, Mad2 and BubR1 and blocked the cells in mitotic phase of the cell cycle. The binding of ansamitocin P3 induced conformational changes in tubulin. A docking analysis suggested that ansamitocin P3 may bind partially to vinblastine binding site on tubulin in two different positions.
12. Ankit Rai, Tilak Kumar Gupta, Sudarshan Kini, Ambarish Kunwar, Avadhesha Surolia, Dulal Panda, CXI-benzo-84 reversibly binds to tubulin at colchicine site and induces apoptosis in cancer cells, Biochemical Pharmacology, Vol. 86, 378 (2013)
2015 Journal Impact Factor = 5.091
In this paper, we discovered that CXI-benzo-84 is a potential anticancer agent from a library of benzimidazole derivatives using cell based screening strategy. CXI-benzo-84 inhibited cell cycle progression in metaphase stage of mitosis and accumulated spindle assembly checkpoint proteins Mad2 and BubR1 on kinetochores, which subsequently activated apoptotic cell death in cancer cells. CXI-benzo-84 depolymerized both interphase and mitotic microtubules, perturbed EB1 binding to microtubules and inhibited the assembly and GTPase activity of tubulin in vitro. Competition experiments and molecular docking suggests that CXI-benzo-84 binds to tubulin at the colchicine-site.
_________________________________Publications before Joining IIT Bombay________________________________
11. Ambarish Kunwar*, Suvranta K Tripathy*, Jing Xu, Michelle K. Mattson, Preetha Anand, Roby Sigua, Michael Vershinin, Richard J. McKenney, Clare C. Yu, Alexander Mogilner†, Steven P. Gross†, Mechanical Stochastic Tug-of-war Models Cannot Explain Bi-directional Lipid droplet Transport, Proceedings of the National Academy of Sciences of the United States of America, Vol. 108, 18960 (2011). *,† Equal Authorship
2011 Journal Impact Factor = 9.681
Experiments suggest that both kinesin and dynein motors have a catch-bond type behavior. Stochastic model predicts correct average detachment time for multiple kinesin and dynein motors. Comparison of theoretical modeling with experiments suggests mechanistic tug-of-war scenarios are inconsistent with observed motion for bi-directional lipid droplet motion.
10. Richard J. McKenney*, Michael Vershinin*, Ambarish Kunwar, Richard B. Vallee† and Steven P. Gross†, LIS1 and NudE Induce a Persistent Dynein Force-Producing State, Cell, Vol. 141, 304 (2010).*,† Equal authorship. On Cover of Cell-April 16, 2010 issue.
2011 Journal Impact Factor = 32.403
Investigates the function of dynein in presence of Lis1 and NudE. NudE alone both recruits dynein to a particular location, but also inactivates it. Lis1 then binds NudE, and the combined Dynein-NudE-Lis1 complex is again active, but now with improved performance. The Dynein-NudE-Lis1 complexes has higher processivity and lower detachment rate under load. This allows each dynein motors to remain attached to the microtubule for longer period under load, which in turn allows multiple motors to work more effectively. In the presence of Lis1 and NudE, the same number of motors can exert a higher average force, not because each motor exerts more force, but rather because on average more motors remain attached to the microtubule.
9. Ambarish Kunwar and Alexander Mogilner, Robust Transport by Multiple Motors with Non-linear Force-Velocity Relations and Stochastic Load Sharing, Physical Biology, Vol. 7, 016012 (2010).
2011 Journal Impact Factor = 2.595
Investigates properties of multiple motor based transport, using both stochastic and mean-field model of load sharing, for motor having non-linear force-velocity curves.
8. Ambarish Kunwar, Michael Vershinin, Jing Xu and Steven P. Gross, Stepping, Strain Gating, and an Unexpected Force-Velocity Curve for Multiple-Motor-Based Transport, Current Biology, Vol. 18, 1173 (2008).
2011 Journal Impact Factor = 9.647
Proposes a stochastic model of load sharing to theoretically investigate how multiple kinesin motors work together. Modeling shows how unequal/stochastic load sharing can result in enhanced performance of multiple motors under load. It also shows that multiple motor function depends strongly on the coupling between individual motors. It also predicts that, surprisingly, for a range of likely cytosolic viscosities, cargos driven by a single motor can move faster than cargos moved by two or more motors. This prediction was later confirmed experimentally.
7. Ambarish Kunwar, Andreas Schadschneider and Debashish Chowdhury, From aggressive driving to molecular motor traffic, Journal of Physics A: Mathematical and General, Vol. 39, 14263 (2006).
Name changed to Journal of Physics A: Mathematical and Theoretical in year 2007
2011 Journal Impact Factor = 1.564
6. Ambarish Kunwar, Debashish Chowdhury, Andreas Schadschneider and Katsuhiro Nishinari, Competition of coarsening and shredding of clusters in a driven diffusive lattice gas, Journal of Statistical Mechanics: Theory and Experiment, P06012 (2006).
2011 Journal Impact Factor = 1.727
5. Pankaj Kumar Mishra, Ambarish Kunwar, Sutapa Mukherji and Debashish Chowdhury, Dynamic instability of microtubules: effect of catastrophe-suppressing drugs, Physical Review E, Vol. 72, 051914 (2005).
(Selected for the November 15, 2005, issue of the Virtual Journal of Biological Physics Research)
2011 Journal Impact Factor = 2.255
4. Dietrich Stauffer, Ambarish Kunwar and Debashish Chowdhury, Evolutionary ecology in-silico: evolving foodwebs, migrating populations and speciation, Physica A: Statistical Mechanics and its Applications, Vol. 352, 202 (2005).
2011 Journal Impact Factor = 1.373
3. Ambarish Kunwar, Evolution of spatially inhomogeneous eco-systems: An unified model based approach, International Journal of Modern Physics C, Vol. 15, 1449 (2004).
2011 Journal Impact Factor = 0.570
2. Ambarish Kunwar, Alexandar John, Katshuhiro Nishinari, Andreas Schadschneider and Debashish Chowdhury, Collective traffic-like movement of ants on a trail: Dynamical phases and phase transitions, Journal of the Physical Society of Japan, Vol. 73, 2979 (2004).
2011 Journal Impact Factor = 2.364
1. Debashish Chowdhury, Dietrich Stauffer and Ambarish Kunwar, Unification of small and large time scales for biological evolution: Deviations from Power law, Physical Review Letters, Vol.90, 068101(2003).
(Selected for the February 15, 2003, issue of the Virtual Journal of Biological Physics Research)
2011 Journal Impact Factor = 7.370