In Silico Modeling of Lovastatin Analogues as Inhibitors of HIV-1 Nef Protein
Currently, no method can completely eliminate the human immunodeficiency virus (HIV) in an infected person. HIV employs an accessory protein called Nef that forms a complex with cellular AP-1, preventing detection of HIV-infected cells. Lovastatin has been recently identified to inhibit the formation of said Nef-AP-1 complex, but its effective concentration is remarked to be far higher than other Nef inhibitors. This study aims to develop a modified lovastatin molecule exhibiting higher binding affinity to the HIV-1 Nef protein than lovastatin in silico. Modified lovastatin molecules based on the interaction map of lovastatin with Nef were modeled, and flexible ligand-flexible receptor docking to the Nef binding site was performed using AutoDock Vina. Residues within the Nef binding site identified by Liu et al. (2019) to be crucial (Glu-63, Val-66, Phe-68, Asp-108, Leu-112, Tyr-115) were set as flexible. Fragment-based drug design was utilized to append molecular fragments to lovastatin in order to maximize its interactions with said crucial residues. From the fragment-based approach, molecule F4 ((1S,3S)‐8‐{2‐[(2R,4R)‐4‐chloro‐6‐oxooxan‐2‐yl]ethyl}‐3‐(hydroxymethyl)‐7‐methyl‐1,2,3,4‐tetrahydronaphthalen‐1‐yl 4‐aminobenzoate) exhibited a binding affinity of -9.0 kcal/mole, and its estimated IC50 ranges between 0.25-0.51 μM which is at least 7.5 times lower than the reported IC50 of lovastatin from literature. This study presents insights on the key modifications to improve lovastatin as an HIV-1 Nef inhibitor and pertinent information about the Nef binding site for future drug development studies.
A.N.T.s: Algorithm for Navigating Traffic System in Automated Warehouses
According to CNN Indonesia 2020, the demand for e-Commerce in Indonesia has nearly doubled during this pandemic. This surge in demand calls for a time-efficient method for warehouse order-picking. One approach to achieve that goal is by incorporating automation in their warehouse systems. Globally, the market of warehouse robotics is expected to reach 12.6 billion USD by 2027 (Data Bridge Market Research, 2020). In this research, the warehouse system studied would utilize AMR (Autonomous Mobile Robots) to lift and deliver movable shelf units to the packing station where workers are at. This research designed a heuristic algorithm called A.N.T.s (Algorithm for Navigating Traffic System) to conduct task assigning and pathfinding for AMR in the automated warehouse. The warehouse layout was drawn as a two-dimensional map in grids. When an order is placed, A.N.T.s would assign the task to a robot that would require the least amount of time to reach the target shelf. A.N.T.s then conducted pathfinding heuristically using Manhattan Distance. A.N.T.s would help the robot to navigate its way to the target shelf unit, lift the shelf and bring it to the designated packing station. A.N.T.s algorithm was tested in various warehouse layouts and with a varying number of AMRs. Comparison against the commonly used Djikstra’s algorithm was also conducted (Shaikh and Dhale, 2013). Results show that the proposed A.N.T.s algorithm could execute 100 orders in a 27x23 layout with five robots 9.96 times faster than Dijkstra with no collisions. The algorithm is also shown to be able to help assign tasks to robots and help them find short paths to navigate their ways to the shelf units and packing stations. A.N.T.s could navigate traffic to avoid deadlocks and collisions in the warehouse with the aid of lanes and directions.
糖果傳遞問題之研究與推廣
n個人圍成一圈,面向圓心,且逆時針編號1,2,……,n。一開始每人手中有一個糖果,由1號開始,逆時針分別給右邊的人一個、兩個、一個、兩個……糖果,手上沒有糖果的人必須退出。我們將此傳遞規則定義為T_1,2,同理T_(1,2⋯,p)。這個傳遞遊戲,最終會有兩種情形,第一種是由一人獨得所有糖果(成功狀態),第二種是數人間傳遞糖果且形成循環(循環狀態)。 研究後得知,在傳遞規則T_(1,2⋯,p) (p≥2)下,若p=〖p_1〗^(α_1 ) 〖p_2〗^(α_2 )⋯〖p_i〗^(α_i )⋯〖p_j〗^(α_j ) ( 為p的相異質因數),任意的n值(n≥p+1)均可唯一表示成n=(p)^t×(〖p_1〗^(s_1 ) 〖p_2〗^(s_2 )⋯〖p_i〗^(s_i )⋅m)+q (t,m∈N, p ∤〖p_1〗^(s_1 ) 〖p_2〗^(s_2 )⋯〖p_i〗^(s_i ), (m,p)=1, q=1,2,⋯,p),令S=(p^t (p-q)+(pq-1))/(p-1)+R⋅p^t,則當m=1時,最終為成功狀態,且獨得糖果者的初始編號為S;當m≥2時,最終為循環狀態,且由m人循環傳遞糖果,而此m人的初始編號是S, S+p^t 〖p_1〗^(s_1 ) 〖p_2〗^(s_2 )⋯〖p_i〗^(s_i ), ⋯⋯ , S+(m-1)⋅p^t 〖p_1〗^(s_1 ) 〖p_2〗^(s_2 )⋯〖p_i〗^(s_i )。上述公式中的R值,可透過我們研究出來的「R值迭代法」求得。更進一步,我們也找出達到成功狀態或循環狀態的最小傳遞數。
Bio-Circular-Green Superabsorber
As the world has become concerned about the global waste crisis and global warming, there has been a surge of research within materials science to find materials that would replace plastic, such as bioplastics or biodegradable materials, in order to reduce environmental pollution. Plastics generates the microplastics that allowed them to become cross contamination enter the ocean through land, sea and river. Science research found (Lusher et al. (2017)) over 220 species of marine animals ingested microplastic, half of them are considered relevant for commercial purpose and increasing the risk of human consumption as it can induce immune response, oxidative stress, cytotoxicity, alter membrane integrity and cause differential expression of genes. Thailand is also experiencing such a challenge, as seen by the overabundance of plastic waste that might take centuries to decompose. For example, around 1680 million personal hygiene products such as diapers, sanitary napkins, and tampons are used each year. This study highlights the use of naturally accessible absorbent fibers from malva nut (Scaphium scaphigerum) (G. Don) Guib & Planch.), which is widely available and biodegradable in nature and has a low carbon footprint. This study also aimed to develop natural absorbent pads using compostable spun, external layers, and biodegradable glue. A prototype sanitary napkin with biodegradable absorbent pads was developed and evaluated for absorption ability, absorption rate, pH, and biodegradability. The absorbent material absorbed up to 19 times its weight in 2 minutes and 33 times its weight in 2 hours, which is enough for an average of 80-150 mL of menstrual blood. The prototype napkin deteriorated within 99 days, based on naked eye observation. Some signs of degradation and microorganisms growing on the prototype were also observed from scanning electron microscopic images. According to the findings, natural absorbent pads made from malva nut have the potential to be converted into sanitary napkins. Furthermore, it is proposed that the components, which include superabsorbent renewable materials, spinning compostable layer, external compostable layer and biodegradable glue, may be used in a variety of goods, including adult diaper pants, incontinence pads, and laboratory bench mats.
Bio-Circular-Green Superabsorber
As the world has become concerned about the global waste crisis and global warming, there has been a surge of research within materials science to find materials that would replace plastic, such as bioplastics or biodegradable materials, in order to reduce environmental pollution. Plastics generates the microplastics that allowed them to become cross contamination enter the ocean through land, sea and river. Science research found (Lusher et al. (2017)) over 220 species of marine animals ingested microplastic, half of them are considered relevant for commercial purpose and increasing the risk of human consumption as it can induce immune response, oxidative stress, cytotoxicity, alter membrane integrity and cause differential expression of genes. Thailand is also experiencing such a challenge, as seen by the overabundance of plastic waste that might take centuries to decompose. For example, around 1680 million personal hygiene products such as diapers, sanitary napkins, and tampons are used each year. This study highlights the use of naturally accessible absorbent fibers from malva nut (Scaphium scaphigerum) (G. Don) Guib & Planch.), which is widely available and biodegradable in nature and has a low carbon footprint. This study also aimed to develop natural absorbent pads using compostable spun, external layers, and biodegradable glue. A prototype sanitary napkin with biodegradable absorbent pads was developed and evaluated for absorption ability, absorption rate, pH, and biodegradability. The absorbent material absorbed up to 19 times its weight in 2 minutes and 33 times its weight in 2 hours, which is enough for an average of 80-150 mL of menstrual blood. The prototype napkin deteriorated within 99 days, based on naked eye observation. Some signs of degradation and microorganisms growing on the prototype were also observed from scanning electron microscopic images. According to the findings, natural absorbent pads made from malva nut have the potential to be converted into sanitary napkins. Furthermore, it is proposed that the components, which include superabsorbent renewable materials, spinning compostable layer, external compostable layer and biodegradable glue, may be used in a variety of goods, including adult diaper pants, incontinence pads, and laboratory bench mats.